Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 1 of 70

1 FORUM ORIGINAL RESEARCH COMMUNICATION

Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila Yun Chen, Megan Sparks, Poonam Bhandari, Scot J. Matkovich and Gerald W. Dorn II

Center for Pharmacogenomics, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.

Running head: Cardiac mitofusin 2 and mitochondrial DNA

Corresponding author: Gerald W Dorn II MD, Philip and Sima K. Needleman Professor and Director, Washington University Center for Pharmacogenomics, 660 S. Euclid Ave., Campus Box 8220, St. Louis, MO 63110. Phone: 314-362-4892. FAX: 314-362-8844. Email:[email protected] Word ct: 4,595 Refs #: 40 Color illustrations: 4 Greyscale illustration: 1

1

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 2 of 70

2

ABSTRACT Aims: Mitofusin (Mfn) 2 redundantly promotes mitochondrial outer membrane tethering and organelle fusion with Mfn1, and uniquely functions as the mitochondrial receptor for Parkin during PINK1-Parkin mediated mitophagy. Selective deletion of Mfn2 with retention of Mfn1 preserves mitochondrial fusion while rendering damaged mitochondria resistant to normal quality control culling mechanisms. Consequently, neuron and cardiomyocyte-specific Mfn2 gene ablation is associated with accumulation of damaged mitochondria and organ dysfunction. Here, we determined how mitochondrial (mt) DNA damage contributes to cardiomyopathy in Mfn2-deficient hearts. Results: RNA sequencing of Mfn2-deficient hearts revealed increased expression of some nuclear-encoded mitochondrial genes, but mitochondrial-encoded transcripts were not upregulated in parallel and mtDNA content was decreased. Ultra-deep sequencing of mtDNA showed no increase in single nucleotide mutations, but copy number variations representing insertion-deletion (in-del) mutations were induced over time by cardiomyocyte-specific Mfn2 deficiency. Double strand mtDNA breaks in the form of indels were confirmed by PCR, and in the form of linear mitochondrial genomes were identified by Southern blot analysis. Linearization of Drosophila cardiomyocyte mtDNA using conditional cardiomyocyte-specific expression of mitochondrial targeted XhoI recapitulated the cardiomyopathy of Mfn2-deficient mouse hearts. Innovation: This is the first description of mitochondrial genome linearization as a causative factor in cardiomyopathy. Conclusion: One of the consequences of interrupting mitochondrial culling by the PINK1Mfn2-Parkin mechanism is an increase in mtDNA double stranded breaks, which adversely impact mitochondrial function and DNA replication. Absatract word count: 227

2

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 3 of 70

3 INTRODUCTION Mitochondrial dynamics encompasses organelle motility, fission, and fusion. Subcellular mitochondrial transport and remodeling of highly interconnected mitochondrial networks through fusion and fission reactions is observed in most cell types (39). Fragmentation of these mitochondrial networks through organelle fission and network regeneration via organelle fusion are necessary to distribute mitochondria to daughter cells during cell mitosis (5). Because cardiomyocyte mitochondria exist as tightly packed and immobile organelles rather than as an interconnected network, and since adult cardiomyocytes have exited the mitotic cycle, these cells do not exhibit the typical requirement for mitochondrial dynamism. Indeed, despite having the largest proportion of mitochondria (~30% by volume) of any cell type, mitochondrial fusion has not been directly observed in adult cardiomyocytes (15). Nevertheless, cardiomyocytes express mitochondrial fusion and fission proteins in abundance, suggesting that there may be noncanonical functions for mitochondrial dynamics factors in this cell type. In adult hearts, interruption of cardiomyocyte mitochondrial fusion by conditional combined genetic ablation of mitofusins (Mfn) 1 and 2 not only induces mitochondrial fragmentation from un-opposed mitochondrial fission, but provokes massive accumulation of abnormal mitochondria (12). Individual deletion of Mfn1 or Mfn2 in cardiac myocytes avoids mitochondrial fragmentation because these two proteins are functionally redundant fusion factors (15,16). Nevertheless, cardiomyocyte Mfn2 deletion (but not Mfn1 deletion) provoked development of unusually large dysmorphic mitochondria, cardiomyocyte respiratory dysfunction, and progressive cardiomyopathy (10). The mechanistic basis by which Mfn2 (but not Mfn1) deficiency evokes accumulation of abnormal mitochondria was revealed through its selectively ablation in mouse livers, hearts, and neurons (10,26,31,33). Together, these studies describe a central role for Mfn2 in mitochondrial quality control, as the essential transduction factor mediating signaling from the mitochondrial PINK1 kinase to the cytosolic E3 ubiquitin ligase Parkin. Given that mitochondrial fusion is preserved when only one Mfn is ablated and the other is retained, the uniquely deleterious effects of

3

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 4 of 70

4 Mfn2 ablation on mitochondrial structure and function appear to be explained by interruption of Parkin-mediated mitophagy. Among the many potential molecular casualties of defective mitochondrial quality control is DNA of mitochondrial genomes (mtDNA). Mitochondria possess ~16.6 kb circular genomes encoding 13 genes of the respiratory chain, plus essential ribosomal and transfer RNAs. Increased mtDNA point mutations and insertion-deletions (in-dels) have been implicated in the skeletal myopathy caused by combined ablation of Mfn1 and Mfn2 (8), but in view of the recent identification of an essential function for Mfn2 in mitophagic mitochondrial culling it is unclear if mtDNA damage occurred as a consequence of defective mitochondrial fusion or interruption of mitophagy. Accordingly, we interrogated mitochondrial genomes before and after appearance of the cardiomyopathy induced by cardiomyocyte-specific Mfn2 gene deletion (10). In contrast to the point mutations that accumulated with mitochondrial fragmentation provoked by combined deletion of Mfn1 and Mfn2 in skeletal muscle, we observed no increase in mtDNA point mutations induced by cardiomyocyte-specific Mfn2 deficiency. We did, however, detect an increase in double stranded mtDNA breaks manifested both as insertion-deletion mutations (in-dels) and linearized genomes, which were associated with loss of cardiac mtDNA. Because linearization of circular mtDNA has not previously been described in cardiomyopathy and its functional implications were unknown, we conditionally expressed a mitochondrialtargeted single cutting DNA restriction enzyme (XhoI) in Drosophila heart tubes. In the fruit fly heart, mtDNA linearization decreased mtDNA content and caused a cardiomyopathy. These studies show that double stranded mtDNA breaks linearize a fraction of mitochondrial genomes which, independent of mtDNA point or in-del mutations, can contribute to end-organ dysfunction.

RESULTS mtDNA defects in Mfn2 deficient hearts. Mfn2 is the essential mitochondrial receptor for Parkin on depolarized mitochondria (10,26). Thus, Mfn2 deficiency produced by cardiac-specific gene ablation interrupts a protective mitophagy pathway, and the resulting accumulation of abnormal 4

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 5 of 70

5 mitochondria impairs cardiomyocyte respiration and induces a progressive cardiomyopathy by 16 weeks of age (10). One of the molecular hallmarks of cardiomyopathy is altered cardiac gene expression (17), but the genetic response to interruption of Mfn2-facilitated cardiac mitophagy has not been described. Accordingly, we used deep RNA sequencing (28) to quantify expression of both nuclear- and mitochondrial-encoded mRNAs before (i.e. in 6 week old mice) and after (i.e. in 16 week old mice) onset of the cardiomyopathy that develops in Mfn2 -deficient mouse hearts. Genome-wide transcriptional profiling identified 7,290 cardiac transcripts expressed at levels of one mRNA copy per cell or greater (raw sequence results were deposited at https://submit.ncbi.nlm.nih.gov/subs/bioproject/, project number SRX285687). Comparison of mRNA expression levels for 6 week and 16 week Mfn2 deficient mouse hearts to their respective age-matched controls identified 1,141 dysregulated (1.3 fold change from control, FDR = 0.01) cardiac-expressed mRNAs (Supplemental Table 1). Unsupervised hierarchical clustering of raw (Figure 1a, left) or normalized (Figure 1a, right) mRNA expression levels perfectly segregated control from Mfn2-deficient hearts. Sixteen week old Mfn2 deficient hearts tended to cluster to the right of their 6 week old Mfn2 null counterparts, suggesting more severe mRNA dysregulation. Indeed, the number of regulated mRNAs changed more than 50, 75, or 100% was significantly greater in 16 week than 6 week Mfn2 null hearts (Chi-Square P < 0.001 for each comparison). Thus, the transcriptional signature evoked by cardiomyocyte-specific Mfn2 deletion precedes the cardiomyopathy and is exaggerated with age. Gene-ontology analysis revealed that a disproportionate number of the dysregulated transcripts belong to functional categories related to mitochondria or metabolism (P < 0.05; Figure 1b), suggesting a primary effect of Mfn2 ablation on cardiac genes involving cellular metabolism. Mitochondria contain approximately 800 nuclear-encoded and just 13 mitochondrial-encoded proteins (21). Of 766 nuclear-encoded mitochondrial proteins listed in www.mitoproteome.org, we detected 650 expressed at 1 mRNA copy per cell or greater in mouse hearts. A disproportionate 28% (183/650; compared to 1141/7290, or 16% of total cardiac transcripts; P =0.01) of these cardiac mitochondrial protein encoding transcripts were dysregulated in Mfn2-deficient hearts (Figure 1c, Supplemental Table

5

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 6 of 70

6 2). Modulated expression of mitochondrial genes anticipated the cardiomyopathy, as it was detected in 6 week old Mfn2 null hearts. Mitochondrial biogenesis is frequently described in heart disease as reactive changes in the expression of genes that direct mtDNA replication and transcription (20,40). We examined the mRNA expression profile induced by cardiomyocyte Mfn2 deficiency for regulated expression of mRNAs encoding factors central to mitochondrial DNA replication and RNA transcription. Expression of several nuclear-encoded mitochondrial biogenesis genes was increased only in 16 week old Mfn2 deficient hearts (Figure 2a). Remarkably, increased expression of some mtDNA replication and transcription factor genes occurred concomitantly with a precipitous decline in the levels of mtDNA relative to nuclear DNA (Figure 2b, left) and loss of cardiomyocyte mitochondrial nucleoids (Figure 2b, middle and right). We hypothesized that increased expression of nuclear-encoded mitochondrial genes was an attempt to compensate for the loss of mitochondrial genomes. Consistent with this notion, levels of the 13 mtDNA-derived transcripts did not increase in parallel with their nuclear-encoded mitochondrial protein counterparts, pointing to a primary failure of mitochondrial gene transcription (Figure 2c). The loss of cardiac mtDNA content, upregulation of some nuclear-encoded mitochondrial transcription and replication factors, and absence of similar upregulation of mitochondrial-derived transcripts, reveal a primary mtDNA defect in Mfn2-deficient hearts. A similar decrease in mtDNA has been observed in Mfn1/Mfn2 double knockout skeletal muscle (8). Since mitochondrial fusion is impaired by combined Mfn1/Mfn2 ablation, but not when Mfn2 is deleted alone, our findings suggest that the mitochondrial genomic defects accrue from interruption of Mfn2-Parkin mediated mitophagy, and not abrogation of mitochondrial fusion. Mitochondrial genomic rearrangements are caused by cardiac Mfn2 ablation. Combined ablation of Mfn1 and Mfn2 in skeletal muscle is postulated to induce skeletal myopathy in part by increasing mtDNA point and in-del mutations (8). We assessed the integrity of mitochondrial genomes in Mfn2-deficient mouse hearts by ultradeep mtDNA resequencing. Because we estimated that mouse myocardium contains ~4,000 mitochondrial genomes for each nuclear genome (see Figure 2b), to assure adequate coverage for mutation detection we resequenced myocardial mitochondrial 6

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 7 of 70

7 genomes (Figure 3a) at an average depth of 101,035 ± 10,180 times per individual mouse heart. There were no differences in the frequency of common or rare single nucleotide sequence variants between wild-type and Mfn2 knockout hearts: mtDNA polymorphisms (defined as variations from the reference sequence having a frequency of 1% or greater) were similar in wild-type and Mfn2-deficient hearts, as expected since polymorphisms tend to be consistent within a given mouse strain (2) (median 72 in wild-type, 66 in Mfn2deficient, Mann-Whitney P=0.15, Figure 3b). We also found no difference in the frequency or distribution of rare mtDNA mutations, either within 966 bp of sequence defined as mtDNA mutational hot spots (median 344 mutations in controls, 350 in 6 wk KO, and 323 in 16 wk KO; P=0.82, Kruskal-Wallis test) Figure 3c) or the remaining mtDNA sequence (median 137 variants in controls, 98 in 6 wk KO, and 101 in 16 wk KO; P=0.92 , KruskalWallis test, Figure 3d). Single nucleotide mutation frequency was similar within mtDNA encoding proteins, rRNA, tRNA, and in the D-loop transcriptional control region (not shown). Mitochondrial DNA single nucleotide mutations are well tolerated, even at high frequencies (37), and so their contribution to mitochondrial dysfunction is likely small. By contrast, regional mtDNA in-dels that remove critical portions of mitochondrial genes are an established cause of disease (34). We therefore examined our mtDNA sequence data for evidence of in-dels, detectable as regional sequence copy number variations (CNV). In control hearts (6 and 16 week), sequence depth was fairly constant across mtDNA regions (Figure 4a, Supplemental Figure 1a). Sequence depth was also similar in 6 week old Mfn2 deficient mtDNA, revealing no evidence of CNV (Supplemental Figure 1a). Remarkably, some mtDNA sequences from 16 week old Mfn2-deficient mouse hearts revealed discrete areas where sequence depth was significantly less (i.e. diverging more that 2 SD) than the mean control depth, identifying discrete genomic deletions (29) (Figure 4a and Supplemental Figure 1b-d). We confirmed that mtDNA deletions occurred only in 16 week old Mfn2-deficient hearts in an independent cohort of samples analyzed by flanking PCR analyses (Figure 4b). Linear mitochondrial genomes accumulate in cardiac Mfn2-deficiency.

7

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 8 of 70

8 A specific mtDNA deletion can cause disease when it deletes a critical portion of an encoded mtRNA, and when it is maternally transmitted and therefore ubiquitous throughout the organism (34). This cannot be the case with the mtDNA deletions we detected in Mfn2 deficient hearts as the causative cardiomyocyte-specific genetic intervention (mfn2 gene ablation) spares the germ cells, and the mtDNA deletions we detected accumulate over time. Furthermore, as revealed by the mtDNA sequence data, deletions appeared stochastically at multiple sites across the mitochondrial genomes, including within a single heart. Thus, these mtDNA in-del mutations almost certainly exhibit marked heteroplasmy, i.e. a mixture of mutant and normal mitochondria within the same cell, and cannot explain the marked mitochondrial abnormalities observed in Mfn2deficient mouse hearts (23). Accordingly, we looked for another explanation. We considered that genomic mtDNA deletions require at least 2 distinct breaks in the circular double stranded mtDNA (to delete part of the genome), followed by mtDNA recircularization and strand repair. By this reasoning, linearization of mtDNA (the inevitable consequence of a single double strand DNA break) is an absolute precondition for forming in-del mtDNA mutations. The effects of mtDNA linearization have not been studied in metazoan mitochondrial dysfunction. In yeast (which have branched linear mitochondrial genomes), double stranded breaks are either repaired or the damaged genomes are cleared (19,27). A similar quality control mechanism likely repairs or eliminates linear metazoan mtDNA. Since mtDNA linearization is a prerequisite for mtDNA deletions, their accumulation in older Mfn2 deficient hearts (vide supra) and Mfn1/Mfn2 double knockout skeletal muscle (8) links the putative mtDNA quality control mechanism to Mfn2-mediated mitochondrial culling. We developed a gel electrophoresis/mtDNA-specific Southern blot procedure to detect linear mtDNA in in vivo heart samples. First, we demonstrated that electrophoresis of intact and XhoI-treated mouse mtDNA (XhoI cuts mtDNA at a single site, thus linearizing it) on 0.5% agarose gels for 20 h at 60 Volts separates linear from intact circular mtDNA; linear mtDNA migrates faster (Figure 4c). We then adapted this Southern blotting approach to total DNA (i.e. combined mitochondrial and nuclear DNA) extracted from mouse myocardium. Linear mtDNA from heart samples co-migrates with XhoI-cut mtDNA, and was detected in 16 week old, but not 6 week old, Mfn2 deficient hearts or control 8

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 9 of 70

9 hearts (Figure 4d, right; arrowheads). Because the experimental samples used whole heart (mixed nuclear and mitochondrial) DNA and we took precautions not to physically damage mtDNA by shearing, etc., intact circular mtDNA is not visualized in the myocardial samples. It is therefore not possible to quantify the proportion of mtDNA that is linear vs non-linear from this experiment. Nevertheless, the high concordance between heart samples with evidence for mtDNA linearization and mtDNA in-del mutations shows that a consequence of cardiac Mfn2-deficiency is accumulation of mtDNA with double stranded breaks.

mtDNA linearization is sufficient to cause mitochondrial cardiomyopathy. The consequences of mtDNA linearization on cardiac homeostasis are unknown. Since we did not detect either mtDNA deletion mutations or linear mtDNA in normal hearts, we considered that normal mtDNA repair mechanisms efficiently re-circularize the linearized mitochondrial genomes or selectively eliminate them, with few cumulative adverse effects. However, the putative mtDNA re-circularization and repair mechanisms may be overwhelmed and mitochondrial integrity compromised when mtDNA damage is severe and/or normal mitophagic clearance mechanisms are suppressed. To test these possibilities we developed Drosophila models conditionally expressing mitochondrialtargeted XhoI in cardiomyocytes (MitoXhoI). As with mouse mtDNA (see Figure 4c), XhoI cleaves Drosophila mtDNA at a single site (in the cytochrome oxidase subunit 1 gene) (38), linearizing mtDNA without deleting any of the mitochondrial genome. Expression of pUASMitoXhoI using a conventional cardiomyocyte-specific tinc4gal4 driver (Figure 5a, left) resulted in almost universal lethality during the second and third instar larval stages and early after pupation. Two escapers that emerged as adults showed severely impaired cardiac function assessed by optical coherence tomography (OCT) (Figure 5a, right), and these flies almost immediately succumbed. Thus, cardiomyocyte-specific MitoXhoI expression established that linear mtDNA is incompatible with normal heart development and function, but early lethality precluded a more detailed characterization of cardiac phenotypes.

9

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 10 of 70

10 To better understand the time-dependent consequences of cardiomyocyte mtDNA linearization we employed a conditional Gal80ts system (Figure 5b, left) to induce MitoXhoI in the heart tubes of adult flies. Flies were bred and allowed to develop through the pupal stage at 19 oC , which does not permit MitoXhoI expression. Newly emerged adults were moved to the expression-permissive temperature of 29oC for three days, which induced cardiomyocyte transgene expression as measured by an enhanced green fluorescent protein (eGFP) marker driven by the same tinc4gal4/Gal80ts system. One week after MitoXhoI induction Drosophila heart tubes exhibited reduced contractility, measured as decreased fractional shortening [%FS], compared to identically treated controls (Figure 5b, right; Figure 5c). This is the fruit fly analog of dilated cardiomyopathy (16). To determine the capacity of fruit fly heart tubes to recover from mtDNA linearization by XhoI we studied a separate cohort of flies two weeks after MitoXho1 induction. Because these flies were placed at the normal maintenance temperature of 23oC after three days at the permissive temperature of 29oC, they had 10 days in which to repair or eliminate the damaged mitochondrial genomes and recover cardiac function. Yet, we observed no functional recovery during this period (Figure 5c). Cardiomyocyte mtDNA was quantified by confocal analysis of mitochondrial nucleoids, and was markedly decreased by XhoI expression (Figure 5d). Together, these results indicate that double strand breaks of mtDNA such as those induced by XhoI-mediated linearization are persistent, are sufficient to deplete cardiomyocyte mtDNA, and will lead to cardiomyopathy.

DISCUSSION Here, in studies of mouse hearts, Drosophila heart tubes, and mitochondrial genomes, we detected double stranded mtDNA breaks after interrupting Mfn2-dependent cardiac mitochondrial quality control. We further demonstrated that mtDNA linearization is sufficient to cause cardiomyopathy. These results reveal deleterious effects of mitochondrial genome linearization, and not just in-del mutations, on mitochondrial homeostasis in the heart.

10

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 11 of 70

11 We tend to conceive of mitochondria as having a life cycle: new mitochondria are formed via “biogenesis” (21), they function for a period of time, and then they become senescent, manifested as depolarization and increased production of toxic reactive oxygen species (ROS) (3). Because senescent mitochondria are cytotoxic, fission/fusion and mitophagy mechanisms have evolved to eliminate them: Dysfunctional mitochondria sequester damaged components into one of two daughter mitochondria formed via assymetrical organelle fission; the defective daughter mitochondrion is then selectively eliminated via mitophagy, whereas the more normal daughter mitochondrion is reintroduced into the cell population via fusion (35). Thus, mitochondrial dynamics and mitochondrial quality control are inextricably related. The current results add the genetic program for producing new mitochondrial proteins, or “mitochondrial biogenesis” into this schema, supporting functional integration of mitochondrial dynamics, biogenesis, and quality control. Mitochondrial DNA mutations have been implicated in myopathic phenotypes in the “mito-mutator mouse”, which expresses a proof-reading defective mitochondrial DNA polymerase (14), and after combined skeletal muscle ablation of Mfn1 and Mfn2 (8). Using ultra-deep resequencing of mitochondrial DNA we did not find evidence that increased mtDNA single nucleotide mutations contribute to the cardiomyopathy caused by cardiac Mfn2 deletion. We believe that lack of causality of single nucleotide variants in the current study is consistent with a number of prior observations: First, mitochondrial mutations in the mito-mutator and skeletal muscle Mfn1/Mfn2 double knockout mice were associated with mitochondrial respiratory compromise and/or dissipation of mitochondrial inner membrane potential, which were not induced by cardiac Mfn2 deficiency (9,10). Second, mitochondrial mutations in genes encoding OXPHOS proteins or tRNAs in the mito-mutator mouse undergo trans-generational clonal expansion to produce mitochondrial respiratory dysfunction and increased reactive oxygen species (1). Because we ablated mfn2 in cardiac myocytes after embryonic development, mtDNA heritability can play no role in our studies. Third, although mtDNA has a mutation rate 10-20 times higher than nuclear DNA (attributed to absence of protective histones and limited repair mechanisms; (4)), the vast majority of mtDNA mutations are functionally recessive (34). Thus, 60-90% of mtDNAs in

11

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 12 of 70

12 heteroplasmic cells can harbor mutations before mitochondrial respiration dysfunction is observed (13,32). Mitochondrial abnormalities induced by interruption of PINK1-Parkin signaling after postnatal cardiomyocyte-specific Mfn2 deletion include increased mitochondrial size (10) and a decline in mtDNA content. The progressive cardiomyopathy of Mfn2 deficiency is therefore linked to replacement of normal mitochondria with larger mitochondria having fewer mitochondrial genomes. The ~16.6 kb mitochondrial genome encodes 13 mitochondrial proteins in addition to 22 transfer RNAs (tRNAs) and 2 ribosomal RNAs (rRNAs). Transcription of mitochondrial-encoded RNAs is bi-directional on the heavy and light mtDNA chains, and would be interrupted by the double stranded DNA breaks that we identified. Although insertions and deletions in mtDNA repair the circular genome structure and therefore permit transcription and replication, linearization of mtDNA likely represents a functional dead-end, interrupting mitochondrial replication which is a critical mitochondrial component of mitochondrial biogenesis (25). We observed that the nuclear mitochondrial biogenesis program increased in apparent compensation. An individual mitochondrion typically has several copies of its genome packaged as discreet nucleoprotein complexes, or nucleoids, that can be exchanged between fused mitochondria in a form of genetic complementation (30). Mitochondrial fusion mediated by Mfn1, Mfn2, and Opa1 also facilitates exchange of mitochondrial gene products, i.e. mtDNA-encoded proteins, tRNAs, and rRNAs. Mixing of mitochondrial inner and outer membranes, nuclear- and mitochondrial-encoded respiratory enzymes, translational and transcriptional machinery, and other matrix components between fused mitochondria temporarily compensates for perturbations of defective genomes, renewing mitochondrial respiratory function. Mitochondria that are excessively damaged, including those with defective genomes, do not undergo fusion-dependent functional complementation and instead are targeted for elimination through the process of mitophagy. In the context of Mfn2 acting as a critical mediator of PINK1-Parkin signaling as well as a mitochondrial fusion factor (10,26,31,33), and the current observation that mtDNA levels plummet in Mfn2-deficient cardiomyopathic hearts, we have re-evaluated our concept of a mitochondrial life cycle. As the descendents of primordial bacteria that developed endosymbiotic relationships with ancestral unicellular organisms, we believe 12

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 13 of 70

13 that mitochondria have no life cycle per se; like the bacteria from which they are descended, mitochondria are immortal. Since there are no “newborn” mitochondria, what is the function of the gene expression program we describe as mitochondrial biogenesis? We propose that nuclear and mitochondrial biogenic programs do not supply new organelles, but instead produce replacement components for functioning mitochondria as they endlessly cycle between renewal and senescence. The current studies indicate that Mfn2, acting as the transducer of PINK1-Parkin mitophagy signaling, helps to maintain the integrity of mitochondrial renewal by preventing accumulation of mtDNA with double stranded breaks. We further demonstrate that mtDNA linearization is sufficient to cause the type of cardiomyopathies that are observed in mice and flies when PINK1-Mfn2-Parkin mediated mitophagy is interrupted (10). We suggest that linearized mtDNA deserves evaluation as a potential contributing factor in other diseases, like Parkinson’s and Alzheimer’s disease, in which defects in mitochondrial quality control apparati can be causative.

INNOVATION Mitochondria are purportedly generated through biogenesis and undergo cyclic fusion and fission that maintains homeostasis until senescent or damaged organelles are eliminated by mitophagy. Here, we unify these three apparently distinct processes by describing a novel consequence of interrupted mitophagy due to ablation of Mfn2, mtDNA linearization. We prove that mtDNA linearization is sufficient to cause cardiomyopathy in fruit flies. We propose that nuclear and mitochondrial biogenic programs do not supply new organelles, but instead produce replacement components for functioning mitochondria as they endlessly cycle between organelle renewal via fusion and elimination of dysfunctional components segregated via asymmetric fission.

MATERIAL AND METHODS

13

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 14 of 70

14 Mouse Generation and Phenotypic Analyses Mfn2 loxp/loxp mice (6,7) were obtained from University of California-Davis and crossed onto the Myh6-nuclear-directed “turbo” Cre line (36) for cardiomyocyte-specific gene deletion after birth. The cardiac phenotype of these mice was described previously (9,10). All experimental procedures were approved by the Animal Studies Committee at Washington University School of Medicine. Transcriptional profiling by deep mRNA sequencing of mouse hearts Transcriptional profiling of Mfn2-KO cardiac tissues was perform by deep mRNA sequencing as described (28). Heat mapping of expression data and statistical analysis used Partek Genomics Suite version 6.4 (Partek, St Louis, Mo). Original RNA sequence data have been deposited at https://submit.ncbi.nlm.nih.gov/subs/bioproject/, project number SRX285687. Mouse mitochondrial genomics analyses Ultra-deep mitochondrial DNA sequencing started with isolated cardiac mitochondria. mtDNA was purified using phenol/chloroform extraction and ethanol precipitation. For each heart, 50-100 ng of mtDNA was randomly fragmented by sonication (Diagenode Bioruptor XL, Denville, NJ). Following column purification (Qiaquick, Qiagen) Illumina sequencing libraries were generated as previously described (28) and single-end sequenced on an Illumina HiSeq. Raw sequence reads (42 nt per read at an average of 67.3 million reads, with 65.3% alignment to the mitochondrial genome) were aligned to the C57BL6/J mitochondrial genome (GenBank: EF108336.1) using Bowtie package version 0.12.7 (24), allowing up to 3 mismatched nucleotides per read while stipulating that each read align to one genomic position only. VarScan version 2.2.3 (22) was used to calculate coverage depth and call variants from aligned reads, using minimum Illumina nucleotide quality scores of 32. The average coverage depth was >100,000; the lowest coverage depth among the mtDNA samples ~40,000, in which a single sequence variant in a single read would be observed at frequency of 0.000025. 30 reads were nominated as a minimum for a confident call, resulting in a minimum detectable frequency of 0.00075 that was used for analysis of all samples. Variants that were not observed on both DNA strands were 14

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 15 of 70

15 censored (~4% of observed variation). Original mtDNA sequence data have been deposited at https://submit.ncbi.nlm.nih.gov/subs/bioproject/, project number SRX285809. To compare the amounts of mtDNA and nuclear DNA, we used quantitative PCR (11). Relative copy number differences are expressed as the difference in amplification cycle threshold, C(t), between mtDNA and nuclear DNA assays (C(t) method). To detect regional deletions in mtDNA, we designed PCR primers to span regions of CNV detected by mtDNA sequencing. Thermopol Taq DNA polymerase system was used for PCR (94°C 30 sec, 60°C 30 sec, 72 °C 1.5 min): Primer pair 1; forward, 5’gccaatgaaatgggaagaaa; reverse, 5’ atgccgtatggaccaacaat (amplifies mtDNA nucleotide 761 to 2884). Primer pair 2; forward, 5’ ggcctcacatcatcactcct, reverse, 5’ ctcgtccgacatgaaggaat (amplifies mtDNA nucleotide 13163 to 14720). Primer pair 3 (negative control); forward, 5’ accagcattccagtcctcac, reverse, 5’ tagggccgcgataataaatg (amplifies mtDNA nucleotide 9410 to 11457). Linearization of mtDNA was detected by mitochondrial DNA-specific Southern blotting of total cardiac DNA (2mg) after size-separation on 0.5% agarose gels (20h at 60V). Intact and XhoI-digested mouse mitochondrial DNA were run as controls. Mitochondrial nucleoids were visualized in isolated murine cardiomyocytes or Drosophila heart tubes by merged confocal microscopy of mitochondria (MitoTracker Red) and DNA (Abcam anti-dsDNA, #ab27156) and quantified using ImageJ. Drosophila lines and cardiac analyses Drosophila melanogaster tub-Gal80ts; tinC4-Gal4 (obtained from Rolf Bodmer, Sanford-Burnham Medical Research Institute, La Jolla, CA) were crossed to UASp-MitoXhoI 2.1/CyO (provided by Patrick O’ Farrell, UCSF, San Francisco, CA) to generate F1 progeny with temperature-inducible cardiomyocyte-specific expression of MitoXhoI. Parental crosses were maintained at 19oC, which does not permit transgene expression. Emerging F1 progeny were collected each day and incubated at 29oC for 3 days for transgene induction, and then shifted to room temperature for maintenance (22-23oC). Expression characteristics of the tub-Gal80ts; tinC4-Gal4 system as a function of these temperatures was monitored with UASp-eGFP (Bloomington stock # 6874). Heart tube contraction was

15

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 16 of 70

16 assessed using optical coherence tomography as described (16,18) at room temperature on 7 and 14 day old flies. Control crosses were set up with w1118 (Bloomington stock #6326). Statistical methods Data are presented as mean ± SEM, except for average mtDNA sequence depth that is depicted as mean ± SD. Paired comparisons between Mfn2-deficient hearts and their age-matched controls used student t-test. Multiple comparisons for mtDNA mutation analyses, in which 6 and 16 week controls were pooled, used one-way ANOVA and Newman-Keuls test, or Kruskal-Wallis tests for nonparametric data. Differences in data distribution were examined using Chi-square test. Statistical difference was defined as P < 0.05. RNA-sequence expression data were analyzed at a false discovery rate of 0.01; p values comparing expression levels of all ~1,100 regulated mRNAs in 6 and 16 week old Mfn2 deficient hearts to their age-matched controls are in Supplemental Table 1. GO category assignment and over-representation used BiNGO.

ACKNOWLEDGEMENTS: Supported in part by NIH grants HL59888 and HL107276.

16

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 17 of 70

17 ABBREVIATIONS: CNV copy number variation FS

fractional shortening

In-del

insertion-deletion

Mfn

mitofusin

mtDNA

mitochondrial DNA

ROS

reactive oxygen species

References 1. 2. 3. 4. 5. 6. 7. 8. 9.

10. 11. 12.

Ameur A, Stewart JB, Freyer C, Hagstrom E, Ingman M, Larsson NG, and Gyllensten U. Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins. PLoS Genet 7: e1002028, 2011. Ashley MV, and Willis CJ. Analysis of mitochondrial DNA polymorphisms among Channel Island deer mice. Evolution 41: 854-63, 1987. Bratic A, and Larsson NG. The role of mitochondria in aging. J Clin Invest 123: 951-7, 2013. Brown WM, George M, Jr., and Wilson AC. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA 76: 1967-71, 1979. Chan DC. Fusion and fission: interlinked processes critical for mitochondrial health. Annu Rev Genet 46: 265-87, 2012. Chen H, Detmer SA, Ewald AJ, Griffin EE, Fraser SE, and Chan DC. Mitofusins Mfn1 and Mfn2 coordinately regulate mitochondrial fusion and are essential for embryonic development. J Cell Biol 160: 189-200, 2003. Chen H, McCaffery JM, and Chan DC. Mitochondrial fusion protects against neurodegeneration in the cerebellum. Cell 130: 548-62, 2007. Chen H, Vermulst M, Wang YE, Chomyn A, Prolla TA, McCaffery JM, and Chan DC. Mitochondrial fusion is required for mtDNA stability in skeletal muscle and tolerance of mtDNA mutations. Cell 141: 280-9, 2010. Chen Y, Csordas G, Jowdy C, Schneider TG, Csordas N, Wang W, Liu Y, Kohlhaas M, Meiser M, Bergem S, Nerbonne JM, Dorn GW 2nd, and Maack C. Mitofusin 2containing mitochondrial-reticular microdomains direct rapid cardiomyocyte bioenergetic responses via interorganelle Ca2+ crosstalk. Circ Res 111: 863-75, 2012. Chen Y, and Dorn GW 2nd. PINK1-phosphorylated mitofusin 2 is a Parkin receptor for culling damaged mitochondria. Science 340: 471-5, 2013. Chen Y, Lewis W, Diwan A, Cheng EH, Matkovich SJ, and Dorn GW 2nd. Dual autonomous mitochondrial cell death pathways are activated by Nix/BNip3L and induce cardiomyopathy. Proc Natl Acad Sci USA 107: 9035-42, 2010. Chen Y, Liu Y, and Dorn GW 2nd. Mitochondrial Fusion is Essential for Organelle Function and Cardiac Homeostasis. Circ Res 109: 1327-31, 2011.

17

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 18 of 70

18 13. 14.

15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. 28. 29. 30.

Chomyn A. The myoclonic epilepsy and ragged-red fiber mutation provides new insights into human mitochondrial function and genetics. Am J Hum Genet 62: 74551, 1998. Dai DF, Chen T, Wanagat J, Laflamme M, Marcinek DJ, Emond MJ, Ngo CP, Prolla TA, and Rabinovitch PS. Age-dependent cardiomyopathy in mitochondrial mutator mice is attenuated by overexpression of catalase targeted to mitochondria. Aging Cell 9: 536-44, 2010. Dorn GW 2nd. Mitochondrial dynamics in heart disease. Biochim Biophys Acta 1833: 233-41, 2013. Dorn GW 2nd, Clark CF, Eschenbacher WH, Kang MY, Engelhard JT, Warner SJ, Matkovich SJ, and Jowdy CC. MARF and Opa1 control mitochondrial and cardiac function in Drosophila. Circ Res 108: 12-7, 2011. Dorn GW 2nd, Robbins J, and Sugden PH. Phenotyping hypertrophy: eschew obfuscation. Circ Res 92: 1171-1175, 2003. Eschenbacher WH, Song M, Chen Y, Bhandari P, Zhao P, Jowdy CC, Engelhard JT, and Dorn GW 2nd. Two rare human mitofusin 2 mutations alter mitochondrial dynamics and induce retinal and cardiac pathology in Drosophila. PloS One 7: e44296, 2012. Gerhold JM, Aun A, Sedman T, Joers P, and Sedman J. Strand invasion structures in the inverted repeat of Candida albicans mitochondrial DNA reveal a role for homologous recombination in replication. Mol Cell 39: 851-61, 2010. Kelly DP. Cell biology: Ageing theories unified. Nature 470: 342-3, 2011. Kelly DP, and Scarpulla RC. Transcriptional regulatory circuits controlling mitochondrial biogenesis and function. Genes Dev 18: 357-368, 2004. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, and Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25: 2283-5, 2009. Kowald A, and Kirkwood TB. Mitochondrial mutations and aging: random drift is insufficient to explain the accumulation of mitochondrial deletion mutants in shortlived animals. Aging Cell, 2013. Langmead B, Trapnell C, Pop M, and Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25, 2009. Lecrenier N, and Foury F. New features of mitochondrial DNA replication system in yeast and man. Gene 246: 37-48, 2000. Lee S, Sterky FH, Mourier A, Terzioglu M, Cullheim S, Olson L, and Larsson NG. Mitofusin 2 is necessary for striatal axonal projections of midbrain dopamine neurons. Hum Mol Genet 21: 4827-35, 2012. Lipinski KA, Kaniak-Golik A, and Golik P. Maintenance and expression of the S. cerevisiae mitochondrial genome--from genetics to evolution and systems biology. Biochim Biophys Acta 1797: 1086-98, 2010. Matkovich SJ, Zhang Y, Van Booven DJ, and Dorn GW 2nd. Deep mRNA sequencing for in vivo functional analysis of cardiac transcriptional regulators: application to Galphaq. Circ Res 106: 1459-67, 2010. Negritto MC. Repairing Double-Strand DNA Breaks. Nature Education 3: 26, 2010. Ono T, Isobe K, Nakada K, and Hayashi JI. Human cells are protected from mitochondrial dysfunction by complementation of DNA products in fused mitochondria. Nat Genet 28: 272-5, 2001. 18

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 19 of 70

19 31. 32. 33.

34. 35. 36. 37. 38. 39. 40.

Pham AH, Meng S, Chu QN, and Chan DC. Loss of Mfn2 results in progressive, retrograde degeneration of dopaminergic neurons in the nigrostriatal circuit. Hum Mol Genet 21: 4817-26, 2012. Rossignol R, Faustin B, Rocher C, Malgat M, Mazat JP, and Letellier T. Mitochondrial threshold effects. Biochem J 370: 751-62, 2003. Sebastian D, Hernandez-Alvarez MI, Segales J, Sorianello E, Munoz JP, Sala D, Waget A, Liesa M, Paz JC, Gopalacharyulu P, Oresic M, Pich S, Burcelin R, Palacin M, and Zorzano A. Mitofusin 2 (Mfn2) links mitochondrial and endoplasmic reticulum function with insulin signaling and is essential for normal glucose homeostasis. Proc Natl Acad Sci USA 109: 5523-8, 2012. Taylor RW, and Turnbull DM. Mitochondrial DNA mutations in human disease. Nat Rev Genet 6: 389-402, 2005. Twig G, and Shirihai OS. The interplay between mitochondrial dynamics and mitophagy. Antioxid Redox Signaling 14: 1939-51, 2011. van Berlo JH, Elrod JW, van den Hoogenhof MM, York AJ, Aronow BJ, Duncan SA, and Molkentin JD. The transcription factor GATA-6 regulates pathological cardiac hypertrophy. Circ Res 107: 1032-40, 2010. Williams SL, Huang J, Edwards YJ, Ulloa RH, Dillon LM, Prolla TA, Vance JM, Moraes CT, and Zuchner S. The mtDNA mutation spectrum of the progeroid Polg mutator mouse includes abundant control region multimers. Cell Metab 12: 675-82, 2010. Xu H, DeLuca SZ, and O'Farrell PH. Manipulating the metazoan mitochondrial genome with targeted restriction enzymes. Science 321: 575-7, 2008. Youle RJ, and van der Bliek AM. Mitochondrial fission, fusion, and stress. Science 337: 1062-5, 2012. Zechner C, Lai L, Zechner JF, Geng T, Yan Z, Rumsey JW, Collia D, Chen Z, Wozniak DF, Leone TC, and Kelly DP. Total skeletal muscle PGC-1 deficiency uncouples mitochondrial derangements from fiber type determination and insulin sensitivity. Cell Metab 12: 633-42, 2010.

19

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 20 of 70

20

FIGURE LEGENDS

20

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 21 of 70

21

Figure 1. Altered gene expression in Mfn2-deficient mouse hearts. (A) Heat map showing unsupervised non-hierarchical clustering of regulated mRNA expression levels in 6 and 16 week old wild-type (ctrl) and Myh6-Cre Mfn2 KO hearts. Each column is a different mouse heart; each row is a different mRNA transcript. Left panel shows raw expression values, right panel shows same expression data normalized for each mRNA. Blue is fewer copies/cell, and red is greater copies/cell. (B) Gene Ontology classification of Mfn2-regulated mRNAs. (C) Unsupervised non-hierarchical clustering heat map of mRNA levels for 183 regulated mitochondrial genes. Left panel shows raw mRNA values, right panel is normalized data. Upregulated TFAM and downregulated mfn2 (the KO gene) are indicated.

21

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 22 of 70

22

22

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 23 of 70

23

Figure 2. Mitochondrial gene expression and mtDNA abnormalities in Mfn2-deficient mouse hearts. (A) mRNA levels, relative to same-age control, of nuclear-encoded mitochondrial transcription factors (left) and replication factors (right) taken from RNA-Seq data in Figure 1. * = significantly different than age-matched controls by group t-test, P values are given on graphs. (B) Cardiomyocyte mitochondria lose mtDNA: (left) qPCR quantitation of mitochondrial-encoded ND2 gene indexed to nuclear-encoded Pecam gene; n=10 per group; (middle) merged confocal analysis of mitochondrial nucleoid content: left cardiomyocyte is from 16 week wild-type control and right cardiomyocyte is from 16 week Myh6-Cre Mfn2

23

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 24 of 70

24 KO. Red is mito-tracker red, green is anti-dsDNA, nuclei are counterstained blue with DAPI. Mitochondrial nucleoids are visible as small yellow/green punctae within red mitochondria. White scale bar is 20 M. Quantitative data (n=3 hearts per group) are to the right. (C) mRNA levels of each of the 13 mitochondrial-genome encoded mitochondrial proteins are not changed in Mfn2 KO hearts.

24

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 25 of 70

25

Figure 3. Cardiac Mfn2 deficiency is not associated with increased myocardial single nucleotide mtDNA sequence variations. (A) Schematic representation of murine mitochondrial genome. Mitochondrial-encoded genes are shown as arrows showing direction of transcription; transfer RNAs are indicated by their single letter amino acid coding. (B) Frequency and position of common polymorphic (allele freq >0.01) nucleotide variations in pooled 6 week (n=4) and 16 week controls (n=3), 6 week Mfn2 KO (n=3), 16 week Mfn2 KO (n=3) hearts. (C) Prevalence and position of rare variants in mutational “hot spots”, i.e. positions where mutations were detected in half of the same sequenced samples. (D) Frequency and position of rare mutations outside of mutational hot spots in the same samples as (C). The distribution of mutations among protein-coding genes, tRNAs, rRNAs, and the D-loop control sequence was the same between genotypes (Supplemental Figure 2).

25

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 26 of 70

26

26

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 27 of 70

27

Figure 4. Accumulation of mtDNA double strand breaks in Mfn2-deficient hearts. (A) Sequence depth for mtDNA sequencing, depicted by nucleotide position across the mitochondrial genome, for the mean of all 16 week control hearts (black) and one of three16 week Mfn2 KO hearts (red). Mitochondrial-encoded genes from Figure 3a are shown in their relative position along the horizontal axis. Arrowheads at top indicate two regions of CNV in the 16 week Mfn2 KO sequence. Horizontal arrows at the bottom show positions of PCR primers used for amplifying across CNV in (B). Other mtDNA sequence data are depicted in Supplemental Figure 1. (B) Accumulation of regional mtDNA deletions in older Mfn2 KO hearts. PCR primers that span mitochondrial genome CNVs detected by sequencing (see panel A) were used for 12 additional independent cardiac mtDNA samples. mtDNA deletions (arrows) were detected in all three 16 week Mfn2 KO hearts. (C) Linear mitochondrial genomes are detected in older Mfn2 KO hearts. Southern blotting of XhoI-linearized mitochondrial-specific mouse heart DNA. (D) Representative (of four per group) Southern blot analysis of mtDNA. Linear genomes are indicated with arrow heads. XhoI-cut mouse cardiac mtDNA is shown on the right (Ctrl). Intact circular mtDNA is not visualized, but equal DNA loading is shown by the faster-migrating nonspecific DNA signals.

27

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 28 of 70

28

28

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 29 of 70

29

Figure 5. mtDNA linearization with MitoXhoI induces cardiomyopathy in Drosophila. (A) (left) Schematic depiction of conventional TincD4-Gal4/pUAS system for cardiacspecific expression of MitoXhoI in Drosophila that was >99% lethal before emergence as adults. (right) Optical coherence tomography (OCT) of a control (Ctrl) and one of two adult cardiac MitoXhoI flies; heart tube function is severely depressed in the MitoXhoI fly. (B) (left) Schematic diagram of temperature inducible system for transient, conditional expression of MitoXhoI in fly cardiomyocytes. (right) Representative OCT of control and conditional MitoXhoI heart tubes 1 week (top) and 2 weeks (bottom) after induction. (C) Group mean data (SEM) for OCT fractional shortening at 1 (n=13/group) and 2 weeks (n=6-8/ group) after transient (3 day) MitoXhoI induction. (D) Merged confocal analysis of mitochondrial nucleoid content: left Drosophila heart tube is from 1 week control and right heart tube is from 1 week after transient cardiac-specific MitoXhoI expression. Red is mitotracker red, green is anti-DNA, nuclei are counterstained blue with DAPI. Mitochondrial

29

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 30 of 70

30

nucleoids are visible as small yellow/green punctae within red mitochondria. White scale

bar is 50 M. Quantitative data (n=3 fly tubes/group) are on the right.

30

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 31 of 70

31 SUPPLEMENTAL DATA

Supplemental Figure 1. Accumulation of mtDNA double strand breaks in 16 wk, but not 6 wk, Mfn2-deficient hearts. (A) Sequence depth for mtDNA sequencing, depicted by nucleotide position across the mitochondrial genome, for the mean of all 16 week control hearts (black) and the mean of all 6 week Mfn2 KO hearts (blue). Error bars show standard deviations. Mitochondrial-encoded genes from Figure 3a are shown in their relative position along the horizontal axis. (B-D) Mean of all 16 week control hearts with standard deviations as in A (black), and individual 16 week Mfn2 KO hearts (red). Arrowheads at top indicate regions of CNV in the 16 week Mfn2 KO sequence (one in panel B, none in panel C, and two in panel D). Panel D is same as Figure 4a, for comparison.

31

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 32 of 70

32 Supplemental Table 1. Relative expression (vs control) of regulated mRNAs in Mfn2deficient hearts. Results are plotted in descending order of regulation in 16 week Mfn2 KO.

Gene Symbol Gdf15 Kcne1 Acta1

Mthfd2 Rasgef1a Ltbp2 Postn Mtap1a A930038C07Rik Cx3cr1 Cdh4 Cilp Gsta1 Dusp26 Uchl1 Wisp2 Cda Arc Kif26b Gck Ankrd1 Prg4 Mfap4 BC022687 Edn3 Krt80 Chac1 Adamtsl2 Col8a1 E2f1 Ncam1

Gene name growth differentiation factor 15 potassium voltage-gated channel, Iskrelated family, member 1 actin, alpha 1, skeletal muscle methylenetetrahydrofolate dehydrogenase (NADP dependent) 2, methenyltetrahydrofolate cyclohydrolase RasGEF domain family, member 1A latent transforming growth factor beta binding protein 2 periostin, osteoblast specific factor microtubule-associated protein 1 A RIKEN cDNA A930038C07 gene chemokine (C-X3-C motif) receptor 1 cadherin 4, type 1, R-cadherin (retinal) cartilage intermediate layer protein, nucleotide pyrophosphohydrolase glutathione S-transferase A1 dual specificity phosphatase 26 (putative) ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) WNT1 inducible signaling pathway protein 2 cytidine deaminase activity-regulated cytoskeletonassociated protein kinesin family member 26B glucokinase (hexokinase 4) ankyrin repeat domain 1 (cardiac muscle) proteoglycan 4 microfibrillar-associated protein 4 cDNA sequence BC022687 endothelin 3 keratin 80 ChaC, cation transport regulator homolog 1 (E. coli) ADAMTS-like 2 collagen, type VIII, alpha 1 E2F transcription factor 1 neural cell adhesion molecule 1

32

6wk fold change 23.2

6 wk p-value 7.34E-05

16wk fold change 48.1

16 wk p-value 8.22E-07

13.7 21.1

6.27E-07 1.46E-03

34.4 28.4

1.14E-09 1.55E-04

11.9 20.5

1.33E-07 5.76E-07

24.9 20.1

3.58E-10 1.53E-07

4.4 2.7 8.5 13.1 3.2 11.6

4.32E-03 2.39E-02 4.19E-08 9.12E-08 2.35E-02 4.31E-04

16.0 15.4 15.3 15.2 14.1 13.4

1.83E-06 4.31E-07 1.38E-10 4.73E-09 6.10E-06 5.16E-05

4.0 25.4

7.76E-04 1.29E-03

13.1 12.7

1.14E-07 1.99E-03

9.9

2.34E-05

11.3

2.64E-06

6.6

1.16E-06

8.7

2.27E-08

3.8 10.6

2.52E-02 9.53E-06

8.7 7.8

2.87E-04 5.50E-06

11.1 7.8 7.7

3.12E-07 1.27E-06 2.70E-05

7.1 6.9 6.3

6.04E-07 3.88E-07 1.07E-05

5.8 3.3 2.4 5.8 4.3 6.1

1.96E-05 3.86E-02 2.12E-03 2.02E-04 7.71E-03 9.30E-04

6.2 6.2 5.9 5.9 5.9 5.8

2.08E-06 1.11E-03 1.66E-07 3.65E-05 5.23E-04 2.97E-04

3.2 1.9 2.4 4.8 3.1

1.47E-02 2.42E-02 5.54E-03 3.97E-04 8.43E-04

5.8 5.7 5.5 5.4 5.2

1.75E-04 9.69E-07 1.63E-06 4.00E-05 3.42E-06

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 33 of 70

33

Slc7a5 Svep1 Ankrd45 Cited1 Mpeg1 Thbs4 Gabrg3 Ttll7 2610019F03Rik Myc Tnfrsf23 Mtap1b Lilrb4 Trib3 Cpxm2 Asns Ctss Apod Lcp1 Mfap5 Ifit3 Ms4a6c Bcl2 Fibin Net1 Ctsk Tubb2a Ube2c Hmgn5 Nppa Atf5 Meox1 Trem2 Haus8 Aif1

solute carrier family 7 (cationic amino acid transporter, y system), member 5 sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 ankyrin repeat domain 45 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1 macrophage expressed gene 1 thrombospondin 4 gamma-aminobutyric acid (GABA) A receptor, gamma 3 tubulin tyrosine ligase-like family, member 7 RIKEN cDNA 2610019F03 genep v-myc myelocytomatosis viral oncogene homolog (avian) tumor necrosis factor receptor superfamily, member 23 microtubule-associated protein 1B leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4 tribbles homolog 3 (Drosophila) carboxypeptidase X (M14 family), member 2 asparagine synthetase cathepsin S apolipoprotein D lymphocyte cytosolic protein 1 (Lplastin) microfibrillar associated protein 5 interferon-induced protein with tetratricopeptide repeats 3 membrane-spanning 4-domains, subfamily A, member 6C B-cell CLL/lymphoma 2 fin bud initiation factor neuroepithelial cell transforming gene 1 cathepsin K tubulin, beta 2A ubiquitin-conjugating enzyme E2C high-mobility group nucleosome binding domain 5 natriuretic peptide precursor A activating transcription factor 5 mesenchyme homeobox 1 triggering receptor expressed on myeloid cells 2 4HAUS augmin-like complex, subunit 8 allograft inflammatory factor 1

33

3.9

2.53E-05

5.2

4.09E-07

2.0 8.1

1.57E-02 1.16E-06

5.1 4.9

1.39E-06 3.15E-06

4.2 2.8 2.5

3.66E-04 3.17E-04 8.75E-03

4.9 4.8 4.7

2.69E-05 4.62E-07 2.02E-05

5.1

2.42E-02

4.7

1.44E-02

3.8 4.9

5.50E-05 1.67E-04

4.6 4.6

1.86E-06 5.34E-05

4.8

7.72E-05

4.5

2.13E-05

3.3 2.6

7.87E-03 1.01E-07

4.4 4.4

4.60E-04 2.01E-11

2.7 2.3

1.90E-02 3.00E-02

4.4 4.4

3.14E-04 1.28E-04

9.5 2.6 2.3 1.9

1.03E-04 1.20E-02 8.15E-04 2.61E-02

4.3 4.3 4.2 4.2

1.27E-03 1.07E-04 2.84E-07 1.03E-05

3.2 1.8

2.19E-04 3.79E-02

4.0 4.0

5.16E-06 1.14E-05

1.9

4.74E-02

4.0

7.16E-05

2.7 3.1 1.9 1.7 1.9 2.1 6.1

1.59E-02 5.06E-07 2.13E-02 7.19E-03 1.19E-02 8.80E-03 4.95E-03

3.9 3.9 3.9 3.9 3.8 3.8 3.7

5.89E-04 5.28E-09 1.13E-05 1.30E-07 3.48E-06 9.00E-06 1.35E-02

1.9 4.0 2.6 1.7

3.26E-02 6.16E-03 2.06E-04 3.43E-02

3.7 3.7 3.7 3.6

3.74E-05 3.39E-03 1.11E-06 8.20E-06

2.3 3.1 4.3

1.96E-02 5.48E-04 2.14E-04

3.6 3.6 3.6

3.15E-04 3.44E-05 4.00E-05

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 34 of 70

34 Rab31 D930014E17Rik Blk Igf1 Grk5 Pacsin1 Emr1 Mt2 Morn4 Fxyd6 Fcrls Mrc1 Eef1a1 Elf4 BC049635 Nqo1 Bgn F13a1 Slc38a1 Hmox1 Cnksr1 Dnajc2 Fgl2 Casp12 Rrp12 Rrm2 Ccrl1 Ipo7 Gstp2 Synpo2l Mak16 Mcm2 Acsf2 Tgfb2 Tmem116 Emp1 Samd10 Pycr1

RAB31, member RAS oncogene family RIKEN cDNA D930014E17 gene B lymphoid tyrosine kinase insulin-like growth factor 1 (somatomedin C) G protein-coupled receptor kinase 5 protein kinase C and casein kinase substrate in neurons 1 egf-like module containing, mucin-like, hormone receptor-like 1 metallothionein 2 MORN repeat containing 4 FXYD domain containing ion transport regulator 6 Fc receptor-like S, scavenger receptor mannose receptor, C type 1 eukaryotic translation elongation factor 1 alpha 1 E74-like factor 4 (ets domain transcription factor) cDNA sequence BC049635 NAD(P)H dehydrogenase, quinone 1 biglycan coagulation factor XIII, A1 polypeptide solute carrier family 38, member 1 heme oxygenase (decycling) 1 connector enhancer of kinase suppressor of Ras 1 DnaJ (Hsp40) homolog, subfamily C, member 2 fibrinogen-like 2 caspase 12 (gene/pseudogene) ribosomal RNA processing 12 homolog (S. cerevisiae) ribonucleotide reductase M2 polypeptide chemokine (C-C motif) receptor-like 1 importin 7 glutathione S-transferase, pi 2 synaptopodin 2-like MAK16 homolog (S. cerevisiae) minichromosome maintenance complex component 2 acyl-CoA synthetase family member 2 transforming growth factor, beta 2 transmembrane protein 116 epithelial membrane protein 1 sterile alpha motif domain containing 10 pyrroline-5-carboxylate reductase 1

34

2.2 1.9 2.9

1.51E-06 1.04E-02 8.43E-04

3.6 3.6 3.6

2.07E-10 3.61E-06 3.07E-05

2.1 2.2

4.47E-03 1.90E-05

3.5 3.5

4.51E-06 4.71E-09

3.2

2.40E-02

3.5

6.14E-03

1.6 3.3 2.9

3.43E-02 4.43E-03 9.14E-04

3.4 3.4 3.4

1.06E-06 1.09E-03 5.04E-05

2.6 1.8 1.6

1.04E-05 3.48E-02 3.24E-02

3.4 3.4 3.3

5.18E-08 2.52E-05 5.34E-06

2.3

5.53E-08

3.3

4.18E-11

2.3 6.9 2.2 1.6 1.5 3.9 2.1

5.22E-07 9.44E-04 1.06E-03 5.90E-03 4.18E-02 2.50E-04 2.62E-02

3.3 3.3 3.3 3.3 3.2 3.2 3.2

3.84E-10 4.25E-03 3.36E-06 1.43E-07 2.65E-06 2.43E-04 4.00E-04

4.1

4.71E-04

3.2

6.18E-04

1.7 2.0 1.9

2.42E-02 2.49E-04 5.00E-02

3.2 3.2 3.2

1.26E-05 1.28E-07 3.36E-04

2.4

1.47E-04

3.2

9.95E-07

6.6 1.9 1.9 5.4 2.0 1.6

1.93E-03 3.47E-02 2.24E-04 1.19E-02 8.53E-04 2.03E-02

3.1 3.1 3.1 3.1 3.1 3.1

2.22E-02 2.03E-04 2.27E-08 4.19E-02 6.11E-07 1.11E-06

3.2 4.1 1.7 4.1 1.6 2.5 2.5

1.63E-03 2.07E-08 2.68E-02 6.07E-06 1.06E-02 8.92E-04 9.24E-03

3.0 3.0 3.0 3.0 3.0 3.0 3.0

6.74E-04 7.03E-08 1.50E-05 1.93E-05 3.43E-07 2.96E-05 6.96E-04

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 35 of 70

35 BC048507 Gpatch4 Txnrd1 Top2b Epn3 Comtd1 Hpgd Ucp2 Ndrg4 Upp1 Sh2d4a Lilrb3 Prkcd Rtn4 Dffa Tspan17 Uck2 Clm3 Malt1 Ppfibp1 Dap Arhgap4 Csf1r Rangap1 Mllt11 Mcm5 Hsp90aa1 Trim47 Strn Slc38a4 S100a13 Tmem106a Fcgr2b Lyz2 Eif2ak2

cDNA sequence BC048507 G patch domain containing 4 thioredoxin reductase 1 topoisomerase (DNA) II beta 180kDa epsin 3 catechol-O-methyltransferase domain containing 1 hydroxyprostaglandin dehydrogenase 15-(NAD) uncoupling protein 2 (mitochondrial, proton carrier) NDRG family member 4 uridine phosphorylase 1 SH2 domain containing 4A leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3 protein kinase C, delta reticulon 4 DNA fragmentation factor, 45kDa, alpha polypeptide tetraspanin 17 uridine-cytidine kinase 2 cytohesin 3 mucosa associated lymphoid tissue lymphoma translocation gene 1 PTPRF interacting protein, binding protein 1 (liprin beta 1) death-associated protein Rho GTPase activating protein 4 colony stimulating factor 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog Ran GTPase activating protein 1 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 11 minichromosome maintenance complex component 5 heat shock protein 90kDa alpha (cytosolic), class A member 1 tripartite motif-containing 47 striatin, calmodulin binding protein solute carrier family 38, member 4 S100 calcium binding protein A13 transmembrane protein 106A Fc fragment of IgG, low affinity IIb, receptor (CD32) lysozyme 2 eukaryotic translation initiation factor 2alpha kinase 2

35

2.1 2.5 2.1 2.3 3.0

3.59E-02 5.62E-05 4.41E-05 2.40E-02 6.44E-05

3.0 2.9 2.9 2.9 2.9

1.51E-03 1.23E-06 9.01E-08 1.71E-03 1.65E-05

2.4

1.85E-02

2.9

1.63E-03

2.5

8.13E-03

2.9

9.79E-04

2.7 1.6 2.9 2.2

9.36E-06 1.81E-03 2.41E-04 6.57E-03

2.9 2.8 2.8 2.8

6.30E-07 6.61E-08 6.20E-05 1.39E-04

2.1 2.2 1.8

1.58E-03 1.89E-04 7.71E-04

2.8 2.8 2.8

1.61E-05 1.44E-06 3.91E-07

2.3 1.9 2.2 2.0

1.59E-05 6.96E-03 5.70E-03 1.27E-02

2.8 2.8 2.8 2.8

1.66E-07 2.73E-05 1.87E-04 2.22E-04

1.7

1.82E-02

2.8

3.35E-05

1.9 2.3 2.2

8.27E-05 5.56E-04 2.09E-02

2.8 2.8 2.7

2.56E-08 1.84E-05 1.71E-03

1.8 2.7

5.59E-04 9.26E-06

2.7 2.7

2.71E-07 1.05E-06

1.9

9.38E-03

2.7

7.49E-05

3.9

2.74E-03

2.7

8.24E-03

1.7 2.0 1.6 2.2 2.1 1.8

1.15E-03 1.98E-03 2.38E-02 2.85E-04 1.03E-04 2.55E-02

2.7 2.7 2.7 2.7 2.7 2.7

3.79E-07 1.17E-05 2.48E-05 5.35E-06 5.87E-07 2.37E-04

2.4 1.7

1.46E-03 5.69E-04

2.7 2.6

1.18E-04 8.82E-08

2.0

1.02E-02

2.6

2.69E-04

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 36 of 70

36 Arl4c Tmem144 P2rx7 Iah1 Cd68 Ahnak2 Phgdh Cdv3 Prss23 Fbn1 6430548M08Rik Mmp23 C1qb Slc39a6 Itih5 Srxn1 Cebpg Atp6v1h C1qa Ttf2 Ptpn6 Mal Mafk Pir Ush1c Ppp1r3c Ccnd2 Anp32b Dpp7 Sephs2 Arsb C1qc Prune2 Ankrd23 Rac2

ADP-ribosylation factor-like 4C transmembrane protein 144 purinergic receptor P2X, ligand-gated ion channel, 7 isoamyl acetate-hydrolyzing esterase 1 homolog (S. cerevisiae) CD68 molecule AHNAK nucleoprotein 2 phosphoglycerate dehydrogenase CDV3 homolog (mouse) protease, serine, 23 fibrillin 1 RIKEN cDNA 6430548M08 gene matrix metallopeptidase 23 complement component 1, q subcomponent, B chain solute carrier family 39 (zinc transporter), member 6 inter-alpha (globulin) inhibitor H5 sulfiredoxin 1 homolog (S. cerevisiae) CCAAT/enhancer binding protein (C/EBP), gamma ATPase, H transporting, lysosomal 50/57kDa, V1 subunit H complement component 1, q subcomponent, A chain transcription termination factor, RNA polymerase II protein tyrosine phosphatase, nonreceptor type 6 mal, T-cell differentiation protein v-maf musculoaponeurotic fibrosarcoma oncogene homolog K (avian) pirin (iron-binding nuclear protein) Usher syndrome 1C (autosomal recessive, severe) protein phosphatase 1, regulatory (inhibitor) subunit 3C cyclin D2 acidic (leucine-rich) nuclear phosphoprotein 32 family, member B dipeptidyl-peptidase 7 selenophosphate synthetase 2 arylsulfatase B complement component 1, q subcomponent, C chain prune homolog 2 (Drosophila) ankyrin repeat domain 23 ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)

36

1.6 2.2

6.03E-03 7.73E-03

2.6 2.6

2.27E-06 4.84E-04

2.2

1.89E-03

2.6

5.81E-05

1.8 2.2 2.3 6.3 2.2 1.4 1.7 3.9 2.0

3.71E-04 1.15E-02 7.00E-05 1.59E-03 7.25E-08 3.75E-02 4.02E-02 6.25E-06 5.48E-03

2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.6 2.5

3.91E-07 8.98E-04 2.52E-06 3.60E-02 4.16E-10 4.14E-06 2.81E-04 6.99E-05 1.53E-04

1.7

5.62E-03

2.5

6.60E-06

2.5 1.6 2.3

5.17E-03 8.83E-03 3.91E-03

2.5 2.5 2.5

1.70E-03 5.22E-06 5.57E-04

1.5

2.65E-02

2.5

2.78E-06

1.6

3.12E-03

2.5

8.50E-07

1.8

1.20E-03

2.5

2.87E-06

2.2

2.32E-02

2.5

4.44E-03

1.7 2.9

1.52E-02 4.17E-04

2.4 2.4

1.05E-04 5.56E-04

1.9 2.3

3.19E-05 1.53E-02

2.4 2.4

5.34E-08 3.85E-03

2.2

6.59E-03

2.4

7.61E-04

1.3 2.5

3.10E-02 4.68E-06

2.4 2.4

1.42E-07 9.64E-07

1.4 1.7 2.5 1.8

2.47E-02 4.38E-02 4.97E-07 2.62E-03

2.4 2.4 2.4 2.4

2.14E-06 4.02E-04 1.45E-07 9.38E-06

1.8 3.2 1.8

2.81E-03 1.68E-04 1.68E-02

2.4 2.4 2.4

9.17E-06 5.68E-04 3.17E-04

2.2

3.53E-02

2.4

8.51E-03

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 37 of 70

37 Adcy7 Polr3g Trmt61a Mtap6 Gpx3 Galns Kcnab2 Plcg2 Gtf3c6 Dmxl2 Ptprf Pld4 Pgd Slc39a11 Gtpbp4 Gm5424 Baiap2l1 P2ry6 Ptgr1 Adap1 Gpx1 Rgs6 E030010A14Rik Tmem35 Ifit2 Casq1 Celsr1 Cst6 Frem2 Ckb Igh-6 Sars Ncf4 Ralgps1

adenylate cyclase 7 polymerase (RNA) III (DNA directed) polypeptide G (32kD) tRNA methyltransferase 61 homolog A (S. cerevisiae) microtubule-associated protein 6 glutathione peroxidase 3 (plasma) galactosamine (N-acetyl)-6-sulfate sulfatase (Morquio syndrome, mucopolysaccharidosis type IVA) potassium voltage-gated channel, shaker-related subfamily, beta member 2 phospholipase C, gamma 2 (phosphatidylinositol-specific) general transcription factor IIIC, polypeptide 6, alpha 35kDa Dmx-like 2 protein tyrosine phosphatase, receptor type, F phospholipase D family, member 4 phosphogluconate dehydrogenase solute carrier family 39 (metal ion transporter), member 11 GTP binding protein 4 argininosuccinate synthase pseudogene 4724 BAI1-associated protein 2-like 1 pyrimidinergic receptor P2Y, G-protein coupled, 6 prostaglandin reductase 1 ArfGAP with dual PH domains 1 glutathione peroxidase 1 regulator of G-protein signaling 6 RIKEN cDNA E030010A14 gene transmembrane protein 35 interferon-induced protein with tetratricopeptide repeats 2 calsequestrin 1 (fast-twitch, skeletal muscle) cadherin, EGF LAG seven-pass G-type receptor 1 (flamingo homolog, Drosophila) cystatin E/M FRAS1 related extracellular matrix protein 2 creatine kinase, brain immunoglobulin heavy constant mu seryl-tRNA synthetase neutrophil cytosolic factor 4, 40kDa Ral GEF with PH domain and SH3

37

1.7

2.58E-03

2.4

5.71E-06

2.5

2.79E-02

2.4

1.65E-02

1.7 1.7 2.3

3.46E-02 2.12E-02 6.22E-08

2.4 2.4 2.3

4.58E-04 1.12E-04 3.72E-09

1.9

8.29E-04

2.3

6.19E-06

2.9

2.47E-02

2.3

3.28E-02

1.9

4.17E-03

2.3

9.72E-05

1.6 2.0

3.21E-02 1.94E-05

2.3 2.3

1.32E-04 1.82E-07

2.0 1.7 2.1

5.11E-05 7.84E-03 9.02E-05

2.3 2.3 2.3

9.34E-07 3.97E-05 2.68E-06

2.9 1.4

9.08E-03 1.94E-02

2.3 2.3

1.47E-02 1.24E-06

2.3 1.7

1.26E-02 1.19E-02

2.3 2.3

3.64E-03 5.92E-05

2.0 2.2 2.8 2.3 1.6 1.5 1.9

2.07E-03 1.12E-02 5.62E-03 7.10E-06 3.17E-02 2.08E-02 3.97E-02

2.3 2.3 2.3 2.3 2.3 2.3 2.3

1.22E-04 2.19E-03 6.85E-03 9.10E-07 1.82E-04 2.42E-05 3.50E-03

2.6

1.03E-03

2.3

9.85E-04

2.2

3.10E-02

2.3

1.30E-02

2.6 3.7

5.51E-06 3.62E-03

2.3 2.3

6.70E-06 2.58E-02

2.1 2.4 1.7 2.2 2.8 3.2

4.38E-04 2.10E-05 7.79E-03 7.47E-07 2.08E-02 1.71E-04

2.2 2.2 2.2 2.2 2.2 2.2

3.08E-05 7.03E-06 8.93E-05 5.26E-08 3.07E-02 1.31E-03

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 38 of 70

38 binding motif 1 Ndn C330016O10Rik Mphosph10 St3gal5 Adamts2 Psip1 Efhd2 Med21 Snx5 Lad1 Tspyl5 Shmt1 Gnb3 Hyal1 Pcolce Eif3a Dpysl3 Slc17a7 Rdh11 Trak2 Shroom3 Myo5a Cobl Hsph1 Fam185a Srbd1 Baiap2 Arhgap9 Dab2 Csf1 Galk2 Pfkp Ctsz Sh3d19 2310030G06Rik Gltp Relt

necdin homolog (mouse) NEDD4 binding protein 3 M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein) ST3 beta-galactoside alpha-2,3sialyltransferase 5 ADAM metallopeptidase with thrombospondin type 1 motif, 2 PC4 and SFRS1 interacting protein 1 EF-hand domain family, member D2 mediator complex subunit 21 sorting nexin 5 ladinin 1 TSPY-like 5 serine hydroxymethyltransferase 1 (soluble) guanine nucleotide binding protein (G protein), beta polypeptide 3 hyaluronoglucosaminidase 1 procollagen C-endopeptidase enhancer eukaryotic translation initiation factor 3, subunit A dihydropyrimidinase-like 3 solute carrier family 17 (sodiumdependent inorganic phosphate cotransporter), member 7 retinol dehydrogenase 11 (all-trans/9cis/11-cis) trafficking protein, kinesin binding 2 shroom family member 3 myosin VA (heavy chain 12, myoxin) cordon-bleu homolog (mouse) heat shock 105kDa/110kDa protein 1 family with sequence similarity 185, member A S1 RNA binding domain 1 BAI1-associated protein 2 Rho GTPase activating protein 9 disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila) colony stimulating factor 1 (macrophage) galactokinase 2 phosphofructokinase, platelet cathepsin Z SH3 domain containing 19 RIKEN cDNA 2310030G06 gene glycolipid transfer protein RELT tumor necrosis factor receptor

38

1.6 2.1

1.01E-02 1.95E-03

2.2 2.2

1.36E-05 2.56E-04

1.8

9.46E-04

2.2

5.82E-06

1.6

2.66E-03

2.2

2.98E-06

1.4 1.7 1.9 1.8 1.5 3.8 2.7

4.96E-02 1.34E-02 5.30E-06 4.15E-02 3.46E-02 1.92E-07 2.66E-02

2.2 2.2 2.2 2.2 2.2 2.2 2.2

6.37E-05 1.05E-04 3.07E-08 2.33E-03 1.09E-04 1.94E-05 4.10E-02

2.9

2.77E-03

2.2

8.26E-03

5.6 2.7 1.6

1.50E-04 1.38E-04 5.90E-03

2.2 2.2 2.2

1.90E-02 3.07E-04 2.25E-05

1.7 1.4

3.15E-06 3.47E-02

2.2 2.2

9.80E-10 3.38E-05

3.3

4.26E-06

2.2

1.05E-04

3.5 1.6 2.0 1.6 2.1 1.8

2.40E-03 8.50E-05 6.78E-05 1.68E-02 1.06E-02 5.93E-03

2.2 2.2 2.1 2.1 2.1 2.1

2.11E-02 5.58E-08 5.95E-06 1.64E-04 2.86E-03 1.96E-04

1.8 2.0 2.2 2.7

1.70E-03 1.01E-02 2.64E-02 1.35E-03

2.1 2.1 2.1 2.1

2.75E-05 2.15E-03 1.72E-02 3.38E-03

1.7

3.08E-02

2.1

8.51E-04

1.6 3.0 1.5 1.4 1.4 2.7 1.7 2.9

8.97E-03 2.07E-06 2.91E-02 1.40E-02 1.39E-02 5.11E-03 1.06E-03 4.58E-03

2.1 2.1 2.1 2.1 2.1 2.1 2.1 2.1

8.90E-05 2.93E-05 6.35E-05 7.00E-06 4.78E-06 1.18E-02 9.30E-06 1.55E-02

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 39 of 70

39 Hagh Hn1l Cox19 Ccnl1 Slc6a6 Atp13a3 Nkain1 Glns-ps1 Gm4798 Glul Pak6 Pi16 1500011H22Rik Capg Tuba1c Scd2 Fuca2 Adck4 Sugt1 Htatip2 Hif1a Tnip1 Dync1li1 Slc19a2 Bag2 Clic5 Asap2 H2-DMa Lnx1 Zfp568 Fbln2 Igfbp6 Sirpa Eif4a-ps4 Anxa5

hydroxyacylglutathione hydrolase hematological and neurological expressed 1-like COX19 cytochrome c oxidase assembly homolog (S. cerevisiae) cyclin L1 solute carrier family 6 (neurotransmitter transporter, taurine), member 6 ATPase type 13A3 Na? transporting ATPase interacting 1 glutamine synthetase pseudogene 1 predicted pseudogene 4798 glutamate-ammonia ligase (glutamine synthetase) p21 protein (Cdc42/Rac)-activated kinase 6 peptidase inhibitor 16 RIKEN cDNA 1500011H22 gene capping protein (actin filament), gelsolin-like tubulin, alpha 1c fucosidase, alpha-L- 2, plasma aarF domain containing kinase 4 SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae) HIV-1 Tat interactive protein 2, 30kDa hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) TNFAIP3 interacting protein 1 dynein, cytoplasmic 1, light intermediate chain 1 solute carrier family 19 (thiamine transporter), member 2 BCL2-associated athanogene 2 chloride intracellular channel 5 ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 histocompatibility 2, class II, locus DMa ligand of numb-protein X 1 zinc finger protein 568 fibulin 2 insulin-like growth factor binding protein 6 signal-regulatory protein alpha eukaryotic translation initiation factor 4A, pseudogene 4 annexin A5

39

1.7

3.40E-05

2.1

1.08E-07

1.9

1.44E-02

2.1

2.05E-03

2.3 1.9

6.23E-05 1.73E-02

2.1 2.1

3.87E-05 3.13E-03

2.3 1.4 1.9 1.7 2.3

7.90E-07 2.99E-02 2.20E-03 5.43E-03 6.51E-03

2.1 2.1 2.1 2.1 2.1

6.17E-07 4.76E-05 2.09E-04 1.04E-04 5.65E-03

2.0

1.54E-04

2.1

1.34E-05

2.1 1.4 1.9

8.55E-03 1.29E-02 9.73E-03

2.1 2.1 2.1

3.48E-03 4.28E-06 1.15E-03

1.4 1.9 2.2 1.7 2.4

4.23E-02 9.51E-03 3.85E-04 1.05E-02 7.56E-03

2.1 2.1 2.0 2.0 2.0

5.93E-05 1.14E-03 1.81E-04 4.09E-04 1.09E-02

1.6 2.4

4.99E-03 1.72E-04

2.0 2.0

3.31E-05 2.61E-04

1.6 2.4

3.99E-02 7.18E-07

2.0 2.0

9.97E-04 1.96E-06

1.5

3.14E-05

2.0

4.06E-09

1.7 1.6 1.4

1.99E-02 3.00E-03 1.14E-02

2.0 2.0 2.0

6.50E-04 7.36E-06 7.42E-06

1.8 1.9 2.3 1.7 1.4

8.05E-04 3.94E-02 6.15E-04 5.48E-03 1.88E-02

2.0 2.0 2.0 2.0 2.0

4.93E-05 1.22E-02 8.22E-04 2.13E-04 1.84E-05

1.4 1.6

4.28E-02 6.35E-04

2.0 2.0

1.23E-04 8.27E-07

1.3 1.6

2.82E-02 1.77E-03

2.0 2.0

4.60E-06 1.36E-05

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 40 of 70

40 Adora1 Scfd1 Crem Fbl Btbd1 Unc93b1 Hn1 Mtmr6 Alpk3 Dnase2a Ube2l6 Man2b2 Csf2ra Prps1 Plekho1 Rps4y2 Ccdc104 Arfgap3 Fads1 Zscan29 Usp39 Pqlc3 Mttp Dhx37 Phlda3 Etv5 Prdx1 Eprs Itgb1bp1 Capza1 Sqstm1 Ppap2c Plbd1 Prmt2 Fam105b Igfals Bhlhe41

adenosine A1 receptor sec1 family domain containing 1 cAMP responsive element modulator fibrillarin BTB (POZ) domain containing 1 unc-93 homolog B1 (C. elegans) hematological and neurological expressed 1 myotubularin related protein 6 alpha-kinase 3 deoxyribonuclease II alpha ubiquitin-conjugating enzyme E2L 6 mannosidase, alpha, class 2B, member 2 colony stimulating factor 2 receptor, alpha, low-affinity (granulocytemacrophage) phosphoribosyl pyrophosphate synthetase 1 pleckstrin homology domain containing, family O member 1 ribosomal protein S4, Y-linked 2 coiled-coil domain containing 104 ADP-ribosylation factor GTPase activating protein 3 fatty acid desaturase 1 zinc finger and SCAN domain containing 29 ubiquitin specific peptidase 39 PQ loop repeat containing 3 microsomal triglyceride transfer protein DEAH (Asp-Glu-Ala-His) box polypeptide 37 pleckstrin homology-like domain, family A, member 3 ets variant gene 5 (ets-related molecule) peroxiredoxin 1 glutamyl-prolyl-tRNA synthetase integrin beta 1 binding protein 1 capping protein (actin filament) muscle Z-line, alpha 1 sequestosome 1 phosphatidic acid phosphatase type 2C phospholipase B domain containing 1 protein arginine methyltransferase 2 family with sequence similarity 105, member B insulin-like growth factor binding protein, acid labile subunit basic helix-loop-helix family, member e41

40

1.7 1.7 3.0 1.6 1.3 1.5

2.44E-02 2.35E-02 9.02E-03 2.84E-02 2.93E-02 7.09E-03

2.0 2.0 2.0 2.0 2.0 2.0

1.53E-03 1.63E-03 4.45E-02 4.71E-04 6.81E-06 1.54E-05

1.7 1.9 1.9 2.0 2.0 2.5

4.31E-03 1.75E-05 9.18E-07 4.14E-03 5.89E-04 1.93E-06

2.0 2.0 2.0 2.0 2.0 2.0

1.44E-04 8.30E-07 6.08E-08 1.62E-03 1.65E-04 1.28E-05

2.1

5.10E-05

2.0

3.04E-05

1.5

3.19E-02

2.0

3.99E-04

1.9 1.7 2.6

1.24E-04 3.56E-03 1.63E-04

2.0 2.0 2.0

8.49E-06 1.06E-04 9.95E-04

1.5 1.6

5.31E-03 1.40E-03

2.0 2.0

1.01E-05 4.55E-06

1.4 1.6 1.7 2.0

3.89E-02 2.52E-02 4.56E-03 2.00E-03

2.0 2.0 2.0 2.0

1.10E-04 9.13E-04 1.35E-04 5.77E-04

2.3

8.18E-07

2.0

1.68E-06

1.5 2.0 1.5 1.6 1.7

2.96E-02 8.89E-04 4.34E-03 5.62E-04 1.03E-02

2.0 1.9 1.9 1.9 1.9

3.79E-04 3.13E-04 6.18E-06 1.78E-06 4.04E-04

1.7 1.9 3.7 1.6 1.9

3.25E-03 1.09E-05 6.63E-04 1.82E-03 1.63E-04

1.9 1.9 1.9 1.9 1.9

1.33E-04 1.39E-06 2.39E-02 2.16E-05 3.41E-05

1.5

1.67E-02

1.9

5.01E-05

2.9

1.71E-03

1.9

1.68E-02

2.1

2.25E-02

1.9

1.72E-02

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 41 of 70

41

Me2 Nuak1 Cacna1a Nupl1 Pde12 Pmepa1 Inpp5j Kif3b Aida Cyb5r1 Elovl1 Anxa7 Nhp2 Prkab2 Ttc27 Gcap14 Nol3 P4hb Ppm1e Phldb2 Abcc4 Cript Cotl1 Vps33b Casc4 1700025G04Rik Pde1c Gba Guk1 Tspo Ppp1r14b Hsn2 Nars Ufsp2 Lipa

malic enzyme 2, NAD()-dependent, mitochondrial NUAK family, SNF1-like kinase, 1 calcium channel, voltage-dependent, P/Q type, alpha 1A subunit nucleoporin like 1 phosphodiesterase 12 prostate transmembrane protein, androgen induced 1 inositol polyphosphate 5-phosphatase J kinesin family member 3B axin interactor, dorsalization associated cytochrome b5 reductase 1 elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 1 annexin A7 NHP2 ribonucleoprotein homolog (yeast) protein kinase, AMP-activated, beta 2 non-catalytic subunit tetratricopeptide repeat domain 27 granule cell antiserum positive 14 nucleolar protein 3 (apoptosis repressor with CARD domain) procollagen-proline, 2-oxoglutarate 4dioxygenase (proline 4-hydroxylase), beta polypeptide protein phosphatase 1E (PP2C domain containing) pleckstrin homology-like domain, family B, member 2 ATP-binding cassette, sub-family C (CFTR/MRP), member 4 cysteine-rich PDZ-binding protein coactosin-like 1 (Dictyostelium) vacuolar protein sorting 33 homolog B (yeast) cancer susceptibility candidate 4 RIKEN cDNA 1700025G04 gene phosphodiesterase 1C, calmodulindependent 70kDa glucosidase, beta; acid (includes glucosylceramidase) guanylate kinase 1 translocator protein (18kDa) protein phosphatase 1, regulatory (inhibitor) subunit 14B hereditary sensory neuropathy, type II asparaginyl-tRNA synthetase UFM1-specific peptidase 2 lipase A, lysosomal acid, cholesterol

41

1.9 1.3

7.51E-04 2.43E-02

1.9 1.9

2.27E-04 5.96E-06

1.9 1.7 1.8

3.00E-02 4.81E-03 7.32E-03

1.9 1.9 1.9

1.20E-02 2.24E-04 1.53E-03

2.0 1.7 1.5 1.8 1.6

6.26E-05 9.49E-03 3.07E-02 8.63E-04 9.43E-03

1.9 1.9 1.9 1.9 1.9

3.01E-05 4.75E-04 6.71E-04 8.63E-05 4.12E-04

1.5 1.6

3.42E-03 2.05E-04

1.9 1.9

2.00E-05 1.19E-06

2.1

1.96E-03

1.9

1.58E-03

1.7 1.6 1.6

9.34E-04 1.33E-02 3.15E-06

1.9 1.9 1.9

2.01E-05 2.48E-04 7.52E-09

1.4

8.29E-04

1.9

6.99E-08

1.4

1.58E-04

1.9

5.12E-09

1.5

2.95E-02

1.9

2.97E-04

1.5

7.11E-03

1.9

2.44E-05

1.7 1.5 1.6

3.03E-03 4.23E-02 3.05E-02

1.9 1.9 1.9

1.36E-04 9.35E-04 1.30E-03

1.7 2.4 1.6

4.79E-02 6.42E-03 2.74E-03

1.9 1.9 1.9

9.80E-03 1.79E-02 6.53E-05

1.7

2.80E-04

1.9

1.03E-05

1.8 1.7 1.7

1.06E-03 1.42E-04 2.79E-03

1.8 1.8 1.8

1.59E-04 5.64E-06 1.39E-04

1.6 1.7 1.4 1.8 1.6

1.55E-02 4.37E-05 1.52E-02 7.25E-03 4.69E-03

1.8 1.8 1.8 1.8 1.8

7.91E-04 1.07E-06 7.38E-05 1.45E-03 1.91E-04

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 42 of 70

42 esterase (Wolman disease) Tbcel Mgmt Gars Fmr1 Rnf141 Ubxn4 Gsr Mid2 Aldh1b1 Pa2g4 Atp8a2 Serpinb6b Ccnd1 Armcx4 F2r Syk Slc3a2 Cidea Ints4 Azin1 Kif5b Ccdc41 Fez2 Eny2 Mfsd1 Slc25a5 Pip4k2a Aox1 Mxra7 Gclc 2610002J02Rik Cct8 Apoe Limk2

tubulin folding cofactor E-like O-6-methylguanine-DNA methyltransferase glycyl-tRNA synthetase fragile X mental retardation 1 ring finger protein 141 UBX domain protein 4 glutathione reductase midline 2 aldehyde dehydrogenase 1 family, member B1 proliferation-associated 2G4, 38kDa ATPase, aminophospholipid transporter-like, class I, type 8A, member 2 serine (or cysteine) peptidase inhibitor, clade B, member 6b cyclin D1 armadillo repeat containing, X-linked 4 coagulation factor II (thrombin) receptor spleen tyrosine kinase solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2 cell death-inducing DFFA-like effector a integrator complex subunit 4 antizyme inhibitor 1 kinesin family member 5B coiled-coil domain containing 41 fasciculation and elongation protein zeta 2 (zygin II) enhancer of yellow 2 homolog (Drosophila) major facilitator superfamily domain containing 1 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5 phosphatidylinositol-5-phosphate 4kinase, type II, alpha aldehyde oxidase 1 matrix-remodelling associated 7 glutamate-cysteine ligase, catalytic subunit RIKEN cDNA 2610002J02 gene chaperonin containing TCP1, subunit 8 (theta) apolipoprotein E LIM domain kinase 2

42

1.3

4.81E-02

1.8

7.57E-05

2.2 1.5 2.5 1.6 1.4 1.5 2.3

3.22E-03 6.58E-03 6.69E-05 1.92E-02 1.65E-02 6.89E-03 8.20E-04

1.8 1.8 1.8 1.8 1.8 1.8 1.8

8.18E-03 3.21E-05 9.44E-04 1.53E-03 1.28E-05 7.82E-05 3.76E-03

3.2 1.4

2.91E-05 1.63E-02

1.8 1.8

3.65E-03 5.50E-05

1.9

4.33E-03

1.8

3.03E-03

1.6 1.8 2.1

1.12E-02 2.82E-03 1.48E-02

1.8 1.8 1.8

4.47E-04 1.28E-03 2.17E-02

1.5 1.4

1.90E-03 3.09E-03

1.8 1.8

9.12E-06 7.99E-06

1.5 1.9 1.8 1.9 1.3 1.4

6.60E-03 9.28E-05 2.28E-05 4.65E-04 5.02E-03 3.20E-02

1.8 1.8 1.8 1.8 1.8 1.8

8.68E-05 8.27E-05 3.72E-06 3.06E-04 1.34E-06 4.52E-04

1.3

2.77E-02

1.8

3.48E-05

1.7

2.95E-02

1.8

6.03E-03

1.8

8.98E-03

1.8

3.58E-03

1.4

3.70E-03

1.8

1.21E-05

1.7 1.8 1.6

4.91E-02 7.08E-04 2.45E-03

1.8 1.7 1.7

2.28E-02 3.27E-04 1.45E-04

1.5 2.7

2.01E-02 5.78E-04

1.7 1.7

3.44E-04 1.19E-02

1.4 1.7 1.7

2.24E-02 1.32E-03 9.59E-04

1.7 1.7 1.7

1.67E-04 1.26E-04 1.26E-04

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 43 of 70

43 Mtss1l Wdr43 Cmklr1 Carhsp1 Mvp Hmha1 Zrsr2 Selplg Elmod2 Syngr1 Tmem176a Flnc Sulf2 Atxn10 Srpk2 Maf Stt3a Rgs12 Usp16 Mtap4 Pdlim1 Mphosph8 Ftl1 Fzd2 Tmem41a Uap1l1 Ino80c Slc11a1 Rfxank Golga4 1810055G02Rik Fam92a Mtdh Ptprk Rexo2 Cdk6 Tmem176b

metastasis suppressor 1-like WD repeat domain 43 chemokine-like receptor 1 calcium regulated heat stable protein 1, 24kDa major vault protein histocompatibility (minor) HA-1 zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2 selectin P ligand ELMO/CED-12 domain containing 2 synaptogyrin 1 transmembrane protein 176A filamin C, gamma (actin binding protein 280) sulfatase 2 ataxin 10 SFRS protein kinase 2 v-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian) STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae) regulator of G-protein signaling 12 ubiquitin specific peptidase 16 microtubule-associated protein 4 PDZ and LIM domain 1 (elfin) M-phase phosphoprotein 8 ferritin light chain 1 frizzled homolog 2 (Drosophila) transmembrane protein 41A UDP-N-acteylglucosamine pyrophosphorylase 1-like 1 INO80 complex subunit C solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1 regulatory factor X-associated ankyrincontaining protein golgi autoantigen, golgin subfamily a, 4 RIKEN cDNA 1810055G02 gene family with sequence similarity 92, member A metadherin protein tyrosine phosphatase, receptor type, K REX2, RNA exonuclease 2 homolog (S. cerevisiae) cyclin-dependent kinase 6 transmembrane protein 176B

43

2.4 1.6 1.5

1.04E-06 4.74E-03 1.67E-02

1.7 1.7 1.7

4.79E-05 2.27E-04 1.12E-03

1.7 1.8 1.6

2.03E-03 2.25E-04 3.07E-03

1.7 1.7 1.7

5.72E-04 1.21E-04 2.19E-04

1.7 2.0 2.3 1.5 1.6

9.79E-03 2.98E-02 3.59E-03 8.45E-06 6.30E-03

1.7 1.7 1.7 1.7 1.7

2.12E-03 4.09E-02 1.75E-02 1.65E-08 8.44E-04

1.6 1.8 1.4 1.5

1.01E-02 2.46E-04 7.08E-03 7.08E-04

1.7 1.7 1.7 1.7

8.27E-04 8.43E-05 5.75E-05 1.70E-05

1.4

2.48E-02

1.7

4.83E-04

1.7 1.8 2.2 1.5 1.7 1.9 1.9 1.5 2.0

1.92E-02 7.39E-04 2.23E-03 1.61E-06 5.99E-03 2.14E-04 4.82E-06 4.84E-02 7.37E-05

1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7

5.22E-03 4.49E-04 1.23E-02 8.93E-09 1.28E-03 4.34E-04 7.27E-06 4.63E-03 2.67E-04

1.7 1.4

3.47E-02 1.99E-03

1.7 1.7

1.72E-02 1.25E-05

2.2

1.41E-02

1.7

4.67E-02

1.6 1.5 1.7

9.40E-03 5.96E-05 8.45E-03

1.7 1.7 1.7

1.22E-03 7.96E-07 4.31E-03

2.0 1.4

2.46E-02 3.70E-02

1.7 1.7

4.98E-02 1.66E-03

1.3

3.45E-02

1.7

7.67E-05

1.5 1.7 1.9

1.74E-02 8.31E-03 2.38E-05

1.7 1.7 1.7

1.37E-03 4.28E-03 2.87E-05

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 44 of 70

44

Scn1b Asl Clic1 Ranbp1 Lrrc27 Wdr1 Tubd1 Prkag3 Slc43a2 Comt1 Cd63 Trp53inp2 Sntb1 Tsen54 Timm10 Atp6v1d Igdcc4 Ddx58 Ftsj3 Cltc Cox8a Slc36a1 D19Bwg1357e Camkk2 Eea1 Atp6v0a1 Lrrc33 Cd151 Impact Kdm5a Gab2 Grn Rnf20 Pdia5 Chd4

sodium channel, voltage-gated, type I, beta argininosuccinate lyase chloride intracellular channel 1 RAN binding protein 1 leucine rich repeat containing 27 WD repeat domain 1 tubulin, delta 1 protein kinase, AMP-activated, gamma 3 non-catalytic subunit solute carrier family 43, member 2 catechol-O-methyltransferase CD63 molecule transformation related protein 53 inducible nuclear protein 2 syntrophin, beta 1 (dystrophinassociated protein A1, 59kDa, basic component 1) tRNA splicing endonuclease 54 homolog (S. cerevisiae) translocase of inner mitochondrial membrane 10 homolog (yeast) ATPase, H transporting, lysosomal 34kDa, V1 subunit D immunoglobulin superfamily, DCC subclass, member 4 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 FtsJ homolog 3 (E. coli) clathrin, heavy chain (Hc) cytochrome c oxidase subunit 8A (ubiquitous) solute carrier family 36 (proton/amino acid symporter), member 1 DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed calcium/calmodulin-dependent protein kinase kinase 2, beta early endosome antigen 1 ATPase, H transporting, lysosomal V0 subunit a1 leucine rich repeat containing 33 CD151 molecule (Raph blood group) Impact homolog (mouse) lysine (K)-specific demethylase 5A GRB2-associated binding protein 2 granulin ring finger protein 20 protein disulfide isomerase family A, member 5 chromodomain helicase DNA binding

44

1.9 1.9 1.4 1.5 1.9 1.4 1.7

8.13E-04 8.36E-03 1.20E-02 1.36E-02 3.20E-02 1.09E-02 9.96E-03

1.7 1.7 1.7 1.7 1.7 1.7 1.7

1.58E-03 1.35E-02 1.71E-04 1.16E-03 3.93E-02 1.66E-04 3.49E-03

2.0 2.5 1.6 1.4

2.63E-02 2.53E-04 8.91E-04 1.20E-02

1.7 1.7 1.7 1.7

4.91E-02 8.24E-03 8.59E-05 8.22E-05

1.4

5.87E-04

1.7

4.17E-07

2.4

4.73E-03

1.7

4.10E-02

1.7

2.45E-02

1.7

9.97E-03

1.7

3.29E-05

1.7

1.51E-05

1.3

3.04E-02

1.7

1.05E-04

1.7

6.28E-04

1.7

3.50E-04

1.4 1.5 1.4

2.60E-02 3.02E-02 1.41E-02

1.6 1.6 1.6

6.28E-04 5.72E-03 1.42E-04

1.4

3.09E-03

1.6

1.21E-05

1.8

8.25E-04

1.6

1.08E-03

1.4

1.33E-02

1.6

3.08E-04

1.6 1.4

5.83E-04 1.90E-02

1.6 1.6

1.03E-04 2.86E-04

1.5 1.7 1.5 1.5 1.4 1.4 1.6 1.4

9.87E-04 2.24E-02 9.03E-05 9.95E-03 3.21E-02 2.54E-03 2.53E-05 3.38E-02

1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6

1.98E-05 1.69E-02 6.41E-07 8.32E-04 1.07E-03 3.52E-05 1.40E-06 6.65E-04

1.7 1.4

2.78E-02 3.40E-04

1.6 1.6

2.44E-02 1.32E-06

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 45 of 70

45 protein 4 Mapt Tbl1xr1 Ddx19b Prkag2 Grhpr Plp2 Eif2s1 Scgb1c1 Rab4b Evc2 Mknk1 Sema3b Slc10a3 Sesn2 Cmas Ubxn1 Zfp346 Pcbp4 Vps41 Atp11a Scamp5 Zcchc4 Obfc2a Engase Sh3bp5 Kcnq4 Dgat1 Rragd Tbrg1 Tssc4 Apc2 Eif2a

microtubule-associated protein tau transducin (beta)-like 1 X-linked receptor 1 DEAD (Asp-Glu-Ala-As) box polypeptide 19B protein kinase, AMP-activated, gamma 2 non-catalytic subunit glyoxylate reductase/hydroxypyruvate reductase proteolipid protein 2 (colonic epithelium-enriched) eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa secretoglobin, family 1C, member 1 RAB4B, member RAS oncogene family Ellis van Creveld syndrome 2 (limbin) MAP kinase interacting serine/threonine kinase 1 sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B solute carrier family 10 (sodium/bile acid cotransporter family), member 3 sestrin 2 cytidine monophosphate Nacetylneuraminic acid synthetase UBX domain protein 1 zinc finger protein 346 poly(rC) binding protein 4 vacuolar protein sorting 41 homolog (S. cerevisiae) ATPase, class VI, type 11A secretory carrier membrane protein 5 zinc finger, CCHC domain containing 4 oligonucleotide/oligosaccharide-binding fold containing 2A endo-beta-N-acetylglucosaminidase SH3-domain binding protein 5 (BTKassociated) potassium voltage-gated channel, KQTlike subfamily, member 4 diacylglycerol O-acyltransferase homolog 1 (mouse) Ras-related GTP binding D transforming growth factor beta regulator 1 tumor suppressing subtransferable candidate 4 adenomatosis polyposis coli 2 eukaryotic translation initiation factor 2A, 65kDa

45

1.5

3.38E-03

1.6

2.68E-04

1.4

1.04E-02

1.6

1.00E-04

1.6

2.82E-03

1.6

7.17E-04

1.8

1.57E-04

1.6

2.49E-04

2.0

3.09E-05

1.6

1.93E-04

1.3

1.27E-02

1.6

5.89E-05

1.5 2.6 1.5 1.7

4.57E-02 4.78E-05 3.29E-02 1.35E-02

1.6 1.6 1.6 1.6

9.10E-03 4.54E-03 4.13E-03 8.74E-03

1.5

5.87E-03

1.6

4.56E-04

1.9

4.88E-07

1.6

2.57E-06

1.5 1.8

2.01E-02 1.67E-02

1.6 1.6

3.41E-03 1.75E-02

1.4 1.3 1.6 1.8

4.18E-02 9.75E-03 2.46E-02 1.57E-04

1.6 1.6 1.6 1.6

1.39E-03 1.97E-05 7.05E-03 1.93E-04

1.3 1.7 2.0 1.5

4.72E-02 1.26E-03 3.72E-04 4.81E-02

1.6 1.6 1.6 1.6

3.24E-04 5.36E-04 2.66E-03 6.08E-03

1.5 2.8

1.35E-02 7.43E-04

1.6 1.6

1.91E-03 3.84E-02

1.8

1.46E-03

1.6

2.88E-03

2.0

4.83E-03

1.6

1.98E-02

1.4 1.7

3.18E-03 2.99E-03

1.6 1.6

2.06E-05 1.92E-03

1.4

2.43E-02

1.6

1.01E-03

1.3 1.5

1.23E-02 1.72E-02

1.6 1.6

1.00E-04 1.56E-03

1.6

2.47E-02

1.6

1.54E-02

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 46 of 70

46 Snx8 Mrap Rgs19 Slk Stk40 Vat1 1110008F13Rik Ppfia1 Ephx1 Hk1 Fkbp15 Usp20 Thrsp Rab3ip Nebl Rab8a Tmf1 Ptpn2 Ralb Scpep1 Chpf Rbm25 Mocs2 Dbnl Dync1i2 Timm9 Fam129b Sbno2 Prpf40a Lgals3bp Rrm1 Itprip Hspb8 Obfc1

sorting nexin 8 melanocortin 2 receptor accessory protein regulator of G-protein signaling 19 STE20-like kinase (yeast) serine/threonine kinase 40 vesicle amine transport protein 1 homolog (T. californica) RIKEN cDNA 1110008F13 gene protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1 epoxide hydrolase 1, microsomal (xenobiotic) hexokinase 1 FK506 binding protein 15, 133kDa ubiquitin specific peptidase 20 thyroid hormone responsive (SPOT14 homolog, rat) RAB3A interacting protein (rabin3) nebulette RAB8A, member RAS oncogene family TATA element modulatory factor 1 protein tyrosine phosphatase, nonreceptor type 2 v-ral simian leukemia viral oncogene homolog B (ras related; GTP binding protein) serine carboxypeptidase 1 chondroitin polymerizing factor RNA binding motif protein 25 molybdenum cofactor synthesis 2 drebrin-like dynein, cytoplasmic 1, intermediate chain 2 translocase of inner mitochondrial membrane 9 homolog (yeast) family with sequence similarity 129, member B strawberry notch homolog 2 (Drosophila) PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) lectin, galactoside-binding, soluble, 3 binding protein ribonucleotide reductase M1 inositol 1,4,5-triphosphate receptor interacting protein heat shock 22kDa protein 8 oligonucleotide/oligosaccharide-binding fold containing 1

46

1.4

2.39E-02

1.6

1.70E-03

1.5 1.7 1.6 1.6

4.75E-02 1.36E-02 7.92E-05 5.50E-04

1.6 1.6 1.6 1.6

9.80E-03 1.37E-02 1.38E-05 2.71E-04

1.3 1.5

1.88E-02 1.01E-02

1.6 1.6

1.53E-04 7.40E-04

1.5

4.09E-02

1.6

5.74E-03

1.5 1.4 1.4 1.4

1.62E-02 2.36E-04 6.91E-03 1.44E-02

1.6 1.6 1.6 1.6

1.65E-03 4.46E-06 2.30E-04 4.00E-04

2.4 1.5 1.4 1.5 1.4

3.77E-05 3.55E-05 1.71E-02 1.11E-02 1.25E-02

1.6 1.6 1.6 1.6 1.6

3.76E-03 5.73E-07 9.27E-04 1.82E-03 1.62E-04

1.5

6.36E-03

1.6

1.44E-03

1.5 1.4 1.6 1.5 1.5 1.7

3.19E-03 3.26E-02 2.92E-04 1.08E-03 8.16E-03 5.63E-04

1.6 1.6 1.6 1.6 1.6 1.6

5.75E-04 1.41E-03 1.67E-04 2.10E-04 1.00E-03 7.19E-04

1.5

3.82E-03

1.6

3.86E-04

1.6

2.30E-02

1.6

1.37E-02

1.5

4.06E-04

1.6

3.41E-05

1.8

6.74E-04

1.6

2.56E-03

1.5

1.01E-02

1.6

1.14E-03

1.6 1.8

1.86E-02 1.91E-02

1.6 1.5

1.44E-02 4.25E-02

1.5 1.4

3.03E-03 2.09E-03

1.5 1.5

8.46E-04 1.69E-05

1.4

4.10E-02

1.5

3.45E-03

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

47

Page 47 of 70

Xrcc6 Parm1 Arf4 Arhgdia Sdc4 Lsm3 Znhit6 Tmem127 Nrtn Lrp1 Taf7 Tmem43 Mt1 Sh3bp4 Fbxo32 Xpot Ckap4 Ank3 Cep350 Pspc1 Pfn2 Pla2g15 Thoc5 Nubp2 Tex2 AU040829 Ap3b1 Prdx4 Lmna Ttc15 Nceh1 Hexa Orc3l Zfp330 BC024814 2310045N01Rik Mea1

X-ray repair complementing defective repair in Chinese hamster cells 6 (Ku autoantigen, 70kDa) prostate androgen-regulated mucin-like protein 1 ADP-ribosylation factor 4 Rho GDP dissociation inhibitor (GDI) alpha syndecan 4 LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) zinc finger, HIT type 6 transmembrane protein 127 neurturin low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor) TAF7 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 55kDa transmembrane protein 43 metallothionein 1 SH3-domain binding protein 4 F-box protein 32 exportin, tRNA (nuclear export receptor for tRNAs) cytoskeleton-associated protein 4 ankyrin 3, node of Ranvier (ankyrin G) centrosomal protein 350kDa paraspeckle component 1 profilin 2 phospholipase A2, group XV THO complex 5 nucleotide binding protein 2 (MinD homolog, E. coli) testis expressed 2 expressed sequence AU040829 adaptor-related protein complex 3, beta 1 subunit peroxiredoxin 4 lamin A/C tetratricopeptide repeat domain 15 arylacetamide deacetylase-like 1 hexosaminidase A (alpha polypeptide) origin recognition complex, subunit 3like (yeast) zinc finger protein 330 cDNA sequence BC024814 RIKEN cDNA 2310045N01 gene male-enhanced antigen 1

47

1.5

1.69E-02

1.5

2.83E-03

1.6 1.3

1.33E-04 1.15E-02

1.5 1.5

4.07E-05 8.60E-05

1.5 1.8

7.73E-04 2.43E-02

1.5 1.5

1.40E-04 4.49E-02

1.4 1.4 1.4 2.5

2.25E-02 1.68E-02 7.93E-04 6.42E-04

1.5 1.5 1.5 1.5

1.57E-03 1.63E-03 4.87E-06 3.56E-02

1.5

1.25E-02

1.5

1.83E-03

1.4 1.4 1.7 1.5 1.5

5.86E-03 1.79E-03 2.22E-02 1.24E-03 2.56E-03

1.5 1.5 1.5 1.5 1.5

2.48E-04 2.49E-05 2.51E-02 1.64E-04 4.09E-04

1.3 1.4 1.4 1.4 1.5 1.3 1.4 1.5

4.36E-02 4.23E-02 1.13E-02 2.41E-02 3.01E-02 4.26E-02 1.10E-02 1.65E-02

1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5

9.01E-04 6.79E-03 2.90E-04 3.76E-03 1.13E-02 2.40E-03 5.13E-04 6.37E-03

1.4 1.5 1.4

2.07E-02 2.30E-03 1.26E-03

1.5 1.5 1.5

8.62E-04 7.75E-04 2.40E-05

1.4 1.5 1.4 1.6 1.8 1.4

4.26E-03 1.49E-02 7.12E-03 1.84E-04 2.07E-04 1.59E-02

1.5 1.5 1.5 1.5 1.5 1.5

7.42E-05 8.14E-03 2.50E-04 2.98E-04 1.19E-03 9.72E-04

1.3 1.5 1.5 1.4 1.3

3.61E-02 2.27E-03 2.95E-02 3.23E-02 2.23E-02

1.5 1.5 1.5 1.5 1.5

1.51E-03 5.28E-04 9.27E-03 2.88E-03 5.16E-04

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 48 of 70

48 Cttn Rnf181 Pak4 Kank2 Cspg4 Snx4 Apex1 Zfp259 Cacnb1 Arid4a Rogdi Aagab Dpp3 Ktn1 Pldn Stxbp1 Slc4a2 C330006K01Rik Dcun1d1 Prkar1a Nsa2 Trim35 Phospho1 Tmco4 Dock8 Atp6v0e2 Creb3 Parn Rnasel Wdr55 Samd8 Gsto1 Cars Snx3 Ehbp1l1

cortactin ring finger protein 181 p21 protein (Cdc42/Rac)-activated kinase 4 KN motif and ankyrin repeat domains 2 chondroitin sulfate proteoglycan 4 sorting nexin 4 APEX nuclease (multifunctional DNA repair enzyme) 1 zinc finger protein 259 calcium channel, voltage-dependent, beta 1 subunit AT rich interactive domain 4A (RBP1like) rogdi homolog (Drosophila) alpha- and gamma-adaptin binding protein dipeptidyl-peptidase 3 kinectin 1 (kinesin receptor) pallidin homolog (mouse) syntaxin binding protein 1 solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1) RIKEN cDNA C330006K01 gene DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae) protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1) NSA2 ribosome biogenesis homolog (S. cerevisiae) tripartite motif-containing 35 phosphatase, orphan 1 transmembrane and coiled-coil domains 4 dedicator of cytokinesis 8 ATPase, H transporting V0 subunit e2 cAMP responsive element binding protein 3 poly(A)-specific ribonuclease (deadenylation nuclease) ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent) WD repeat domain 55 sterile alpha motif domain containing 8 glutathione S-transferase omega 1 cysteinyl-tRNA synthetase sorting nexin 3 EH domain binding protein 1-like 1

48

1.6 1.4

1.08E-02 5.99E-03

1.5 1.5

7.71E-03 8.12E-04

1.4 1.4 1.4 1.3

3.27E-02 6.27E-05 1.09E-02 1.50E-02

1.5 1.5 1.5 1.5

7.39E-03 3.61E-07 9.43E-04 2.64E-04

1.8 1.5

3.76E-04 6.66E-04

1.5 1.5

2.88E-03 3.90E-04

1.5

1.25E-02

1.5

6.35E-03

1.5 2.0

1.91E-02 3.15E-03

1.5 1.5

7.68E-03 2.99E-02

1.5 1.3 1.3 1.7 1.6

4.16E-03 2.80E-02 3.13E-02 8.07E-03 2.94E-03

1.5 1.5 1.5 1.5 1.5

2.65E-03 1.14E-03 1.64E-03 1.53E-02 4.70E-03

1.4 2.1

1.61E-02 2.08E-05

1.5 1.5

2.62E-03 2.84E-03

1.6

2.23E-02

1.5

3.53E-02

1.5

2.10E-04

1.5

7.26E-05

1.4 1.3 1.4

3.29E-04 3.08E-03 4.77E-02

1.5 1.5 1.5

3.04E-05 5.31E-05 1.66E-02

1.5 1.5 1.5

5.79E-03 1.11E-02 1.08E-04

1.5 1.5 1.5

4.82E-03 4.74E-03 4.82E-05

1.3

4.25E-02

1.5

2.72E-03

1.4

3.40E-02

1.5

1.36E-02

1.5 1.6 1.4 1.4 1.8 1.4 1.4

4.13E-02 1.22E-02 2.80E-02 2.23E-02 2.10E-03 2.42E-03 7.06E-03

1.5 1.5 1.5 1.5 1.5 1.4 1.4

3.27E-02 1.56E-02 7.96E-03 2.61E-03 1.53E-02 2.64E-04 5.65E-04

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 49 of 70

49 Sepx1 Bysl Stambp Plxna1 Def8 Ndrg3 Becn1 Abhd4 Synm Pld3 Utp11l Fam96a Irgq Mdga1 Pfn1 Nagpa Plscr1 Cdc2l1 Cat Plin2 Sec61a1 Pfkfb3 Adamtsl5 Pcgf3 Shfm1 Atg13 Sh3bp1 Snx6 Dusp3 Dcaf5 Paqr7 Pdcd6 Cox6a1 Ndel1 Myo9b Ascc2 Atpif1 Bop1

selenoprotein X, 1 bystin-like STAM binding protein plexin A1 differentially expressed in FDCP 8 homolog (mouse) NDRG family member 3 beclin 1, autophagy related abhydrolase domain containing 4 synemin, intermediate filament protein phospholipase D family, member 3 UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast) family with sequence similarity 96, member A immunity-related GTPase family, Q MAM domain containing glycosylphosphatidylinositol anchor 1 profilin 1 N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase phospholipid scramblase 1 cell division cycle 2-like 1 (PITSLRE proteins) catalase perilipin 2 Sec61 alpha 1 subunit (S. cerevisiae) 6-phosphofructo-2-kinase/fructose-2,6biphosphatase 3 ADAMTS-like 5 polycomb group ring finger 3 split hand/foot malformation (ectrodactyly) type 1 ATG13 autophagy related 13 homolog SH3-domain binding protein 1 sorting nexin 6 dual specificity phosphatase 3 DDB1 and CUL4 associated factor 5 progestin and adipoQ receptor family member VII programmed cell death 6 cytochrome c oxidase subunit VIa polypeptide 1 nudE nuclear distribution gene E homolog (A. nidulans)-like 1 myosin IXB activating signal cointegrator 1 complex subunit 2 ATPase inhibitory factor 1 block of proliferation 1

49

1.5 1.4 1.4 1.3

1.99E-03 3.63E-02 4.18E-02 4.84E-02

1.4 1.4 1.4 1.4

1.40E-03 7.39E-03 1.24E-02 6.91E-03

1.4 1.5 1.6 1.6 1.8 1.6

3.54E-03 2.78E-02 4.20E-05 4.18E-06 4.34E-04 6.21E-03

1.4 1.4 1.4 1.4 1.4 1.4

3.64E-04 2.77E-02 5.67E-05 1.21E-05 5.12E-03 1.58E-02

1.5

1.18E-02

1.4

1.18E-02

1.8 1.5

3.16E-03 1.50E-03

1.4 1.4

2.18E-02 1.52E-03

1.7 1.5

2.55E-03 3.33E-03

1.4 1.4

9.95E-03 1.42E-03

1.9 1.9

3.56E-04 5.60E-04

1.4 1.4

1.17E-02 1.20E-02

1.3 1.5 1.4 1.3

1.12E-02 1.27E-04 2.35E-02 1.12E-02

1.4 1.4 1.4 1.4

3.49E-04 1.74E-04 8.61E-03 3.84E-04

1.9 1.4 1.4

3.36E-03 1.08E-02 3.06E-03

1.4 1.4 1.4

3.51E-02 3.05E-03 6.08E-04

1.5 1.4 1.6 1.4 1.6 1.3

7.63E-04 8.31E-03 1.79E-02 2.88E-02 6.23E-05 1.07E-03

1.4 1.4 1.4 1.4 1.4 1.4

7.24E-04 1.11E-03 3.03E-02 5.85E-03 4.17E-04 5.05E-05

1.7 1.3

1.08E-03 1.96E-02

1.4 1.4

5.72E-03 2.69E-03

1.3

2.53E-02

1.4

1.67E-03

1.4 1.3

2.80E-02 1.68E-02

1.4 1.4

8.73E-03 2.51E-03

1.4 1.6 1.4

1.80E-04 1.98E-04 2.37E-02

1.4 1.4 1.4

6.36E-05 1.48E-03 7.71E-03

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 50 of 70

50 Ipo4 Cyb5r3 Slc38a3 Sepw1 Wbp5 Stap2 Fkbp10 Mapre3 Igsf3 Hspbp1 Rasa3 Lonp1 Tnfrsf1b Gtf2h1 Rad17 Ttc1 D730040F13Rik Asxl1 Psmb10 Aprt Rbbp7 Aimp2 Mtap1s Ubiad1 Rbm45 Synpo Parp4 Flt4 Tulp4 Arl8a Mdc1 Cul7 AI462493 Gpx4 Psenen Slc25a37 Pyroxd2 Rnf4

importin 4 cytochrome b5 reductase 3 solute carrier family 38, member 3 selenoprotein W, 1 WW domain binding protein 5 signal transducing adaptor family member 2 FK506 binding protein 10, 65 kDa microtubule-associated protein, RP/EB family, member 3 immunoglobulin superfamily, member 3 hsp70-interacting protein RAS p21 protein activator 3 lon peptidase 1, mitochondrial tumor necrosis factor receptor superfamily, member 1B general transcription factor IIH, polypeptide 1, 62kDa RAD17 homolog (S. pombe) tetratricopeptide repeat domain 1 RIKEN cDNA D730040F13 gene additional sex combs like 1 (Drosophila) proteasome (prosome, macropain) subunit, beta type, 10 adenine phosphoribosyltransferase retinoblastoma binding protein 7 aminoacyl tRNA synthetase complexinteracting multifunctional protein 2 microtubule-associated protein 1S UbiA prenyltransferase domain containing 1 RNA binding motif protein 45 synaptopodin poly (ADP-ribose) polymerase family, member 4 fms-related tyrosine kinase 4 tubby like protein 4 ADP-ribosylation factor-like 8A mediator of DNA damage checkpoint 1 cullin 7 expressed sequence AI462493 glutathione peroxidase 4 (phospholipid hydroperoxidase) presenilin enhancer 2 homolog (C. elegans) solute carrier family 25, member 37 pyridine nucleotide-disulphide oxidoreductase domain 2 ring finger protein 4

50

1.5 1.4 1.5 1.6 1.4

4.71E-02 4.69E-03 3.42E-02 6.71E-04 4.39E-02

1.4 1.4 1.4 1.4 1.4

4.07E-02 1.40E-03 4.84E-02 2.82E-03 1.64E-02

1.5 1.5

3.77E-03 3.93E-02

1.4 1.4

7.99E-03 4.08E-02

1.7 1.6 1.4 1.5 1.4

4.06E-06 2.29E-03 4.20E-02 4.22E-02 5.48E-03

1.4 1.4 1.4 1.4 1.4

1.12E-04 9.06E-03 2.28E-02 3.88E-02 1.39E-03

1.5

2.59E-02

1.4

2.63E-02

1.3 1.5 1.6 1.4 1.4

4.71E-02 1.47E-03 2.61E-03 1.48E-02 3.95E-03

1.4 1.4 1.4 1.4 1.4

7.60E-03 2.10E-03 1.52E-02 1.24E-02 8.42E-04

1.6 1.4 1.3

8.45E-03 4.05E-02 5.22E-03

1.4 1.4 1.4

2.58E-02 2.74E-02 4.49E-04

1.5 1.4

9.10E-03 1.47E-02

1.4 1.4

2.14E-02 1.21E-02

1.4 1.5 1.4

1.73E-02 2.61E-02 7.62E-03

1.4 1.4 1.4

8.87E-03 2.88E-02 5.01E-03

1.6 1.6 1.3 1.4 1.5 1.5 1.3

3.76E-04 2.38E-04 8.44E-03 1.02E-02 7.32E-03 1.39E-02 4.56E-02

1.4 1.4 1.4 1.4 1.4 1.4 1.4

1.71E-03 1.29E-03 9.20E-04 8.58E-03 1.67E-02 2.64E-02 1.06E-02

1.6

1.64E-04

1.4

1.71E-03

1.5 2.1

6.90E-04 1.93E-05

1.4 1.4

2.83E-03 9.43E-03

1.8 1.3

1.08E-03 1.72E-02

1.4 1.4

2.16E-02 2.77E-03

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 51 of 70

51 Mrps23 Rraga Nop14 Stat2 Smarcc1 Vac14 Eya3 Tln1 Tbx20 Mfsd6 N28178 1110008P14Rik Sox12 Xpc Rbm4 9530068E07Rik Slc25a23 Pwwp2b Optn Plxnb2 Pgm5 Ywhag Snap47 Uba5 Tmem98 Blmh Rab3d Creg1 Isy1 Zfyve20 Slc6a8 Adipor2 Kbtbd5 Fgfrl1 Med15

mitochondrial ribosomal protein S23 Ras-related GTP binding A NOP14 nucleolar protein homolog (yeast) signal transducer and activator of transcription 2, 113kDa SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1 Vac14 homolog (S. cerevisiae) eyes absent homolog 3 (Drosophila) talin 1 T-box 20 major facilitator superfamily domain containing 6 expressed sequence N28178 RIKEN cDNA 1110008P14 gene SRY (sex determining region Y)-box 12 xeroderma pigmentosum, complementation group C RNA binding motif protein 4 RIKEN cDNA 9530068E07 gene solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23 PWWP domain containing 2B optineurin plexin B2 phosphoglucomutase 5 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide synaptosomal-associated protein, 47 ubiquitin-like modifier activating enzyme 5 transmembrane protein 98 bleomycin hydrolase RAB3D, member RAS oncogene family cellular repressor of E1A-stimulated genes 1 ISY1 splicing factor homolog (S. cerevisiae) zinc finger, FYVE domain containing 20 solute carrier family 6 (neurotransmitter transporter, creatine), member 8 adiponectin receptor 2 kelch repeat and BTB (POZ) domain containing 5 fibroblast growth factor receptor-like 1 mediator complex subunit 15

51

1.6 1.4

1.34E-04 1.49E-02

1.4 1.4

2.12E-03 8.43E-03

1.4

9.35E-03

1.4

1.14E-02

1.6

1.26E-03

1.4

1.09E-02

1.3 1.5 1.5 1.4 1.3

9.50E-04 1.98E-02 7.20E-03 8.45E-03 3.94E-03

1.4 1.4 1.4 1.4 1.4

9.55E-05 2.62E-02 2.16E-02 5.10E-03 5.26E-04

1.4 2.0 1.6 1.6

2.90E-02 1.80E-05 4.87E-03 4.43E-03

1.3 1.3 1.3 1.3

1.57E-02 7.46E-03 2.74E-02 3.55E-02

1.6 1.3 1.5

2.18E-05 4.89E-02 1.15E-02

1.3 1.3 1.3

7.06E-04 1.66E-02 2.27E-02

1.5 1.5 1.4 1.4 1.5

9.08E-04 5.21E-03 4.37E-03 5.14E-03 2.53E-03

1.3 1.3 1.3 1.3 1.3

5.44E-03 1.55E-02 5.92E-03 4.26E-03 9.13E-03

1.3 1.4

7.20E-03 4.75E-03

1.3 1.3

2.75E-03 3.73E-03

1.5 1.3 1.4 2.1

2.91E-02 3.82E-02 3.86E-02 1.65E-04

1.3 1.3 1.3 1.3

4.92E-02 1.65E-02 4.03E-02 4.92E-02

1.5

1.44E-02

1.3

2.86E-02

1.5 1.4

7.87E-03 3.15E-02

1.3 1.3

1.77E-02 2.39E-02

1.4 1.5

1.58E-04 2.05E-04

1.3 1.3

9.97E-05 1.08E-03

1.7 1.6 1.3

1.88E-03 8.93E-05 2.74E-03

1.3 1.3 1.3

4.27E-02 2.23E-03 9.94E-04

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 52 of 70

52 R3hcc1 Porcn Pigq Armc5 Dtymk Serf2 Ttll5 Vps37c Ak2 Nploc4 Wdr91 Dgka Ankrd9 Ctnna3 Tmem182 Cox6c Gon4l Grcc10 Eef2k Slc25a26 Prkce Dtna Arap3 Lphn2 Pnrc1 Sgcg Mylk Ubr2 Atxn1 Ndufa2 Atp5k Fyn Mrpl27 Tomm40l Setbp1 Tmem159 Sdpr

R3H domain and coiled-coil containing 1 porcupine homolog (Drosophila) phosphatidylinositol glycan anchor biosynthesis, class Q armadillo repeat containing 5 deoxythymidylate kinase (thymidylate kinase) small EDRK-rich factor 2 tubulin tyrosine ligase-like family, member 5 vacuolar protein sorting 37 homolog C (S. cerevisiae) adenylate kinase 2 nuclear protein localization 4 homolog (S. cerevisiae) WD repeat domain 91 diacylglycerol kinase, alpha 80kDa ankyrin repeat domain 9 catenin (cadherin-associated protein), alpha 3 transmembrane protein 182 cytochrome c oxidase subunit VIc gon-4-like (C. elegans) gene rich cluster, C10 gene eukaryotic elongation factor-2 kinase solute carrier family 25, member 26 protein kinase C, epsilon dystrobrevin, alpha ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3 latrophilin 2 proline-rich nuclear receptor coactivator 1 sarcoglycan, gamma (35kDa dystrophinassociated glycoprotein) myosin light chain kinase ubiquitin protein ligase E3 component n-recognin 2 ataxin 1 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa ATP synthase, H+ transporting, mitochondrial F1F0 complex, subunit e FYN oncogene related to SRC, FGR, YES mitochondrial ribosomal protein L27 translocase of outer mitochondrial membrane 40 homolog (yeast)-like SET binding protein 1 transmembrane protein 159 serum deprivation response

52

1.5 1.5

1.43E-02 1.41E-02

1.3 1.3

4.49E-02 4.89E-02

1.3 1.7

7.19E-03 4.95E-04

1.3 1.3

4.25E-03 1.68E-02

1.3 1.4

2.93E-02 4.75E-02

1.3 1.3

1.49E-02 4.91E-02

1.6

3.53E-03

1.3

4.52E-02

1.5 1.3

6.86E-04 2.50E-03

1.3 1.3

7.56E-03 1.87E-03

1.5 1.6 -1.4 -1.4

5.13E-04 3.51E-03 6.92E-03 1.41E-02

1.3 1.3 -1.3 -1.3

3.43E-03 3.96E-02 1.57E-02 2.70E-02

-1.4 -1.4 -1.4 -1.3 -1.4 -1.5 -1.5 -1.4 -1.6

1.16E-02 6.33E-03 1.56E-03 1.59E-02 1.26E-02 1.05E-02 1.09E-03 2.60E-02 5.03E-04

-1.3 -1.3 -1.3 -1.3 -1.3 -1.3 -1.3 -1.3 -1.3

2.22E-02 4.66E-03 1.06E-03 4.92E-03 1.31E-02 2.22E-02 5.87E-03 1.53E-02 8.83E-03

-1.4 -1.3

6.75E-03 9.30E-03

-1.3 -1.3

1.07E-02 2.18E-03

-1.4

2.68E-02

-1.3

1.60E-02

-1.5 -1.4

1.46E-03 4.95E-03

-1.3 -1.3

3.98E-03 2.58E-03

-1.4 -1.5

5.74E-03 5.50E-03

-1.3 -1.4

5.11E-03 1.45E-02

-1.4

6.27E-03

-1.4

2.46E-03

-1.3 -1.7 -1.5

1.21E-02 5.22E-05 5.62E-03

-1.4 -1.4 -1.4

2.73E-03 2.59E-03 8.66E-03

-1.4 -1.4 -1.4 -1.4

8.38E-03 6.46E-03 1.34E-02 5.06E-05

-1.4 -1.4 -1.4 -1.4

4.21E-03 5.22E-03 1.22E-02 1.04E-05

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 53 of 70

53 (phosphatidylserine binding protein) Glg1 Oat Jph2 Cox8b She Nfia Khdrbs3 S1pr3 Maf1 Mrps36 5930434B04Rik Kcnj8 Lpin1 E130203B14Rik Myh11 3110057O12Rik Deaf1 Trim63 Ehhadh Lsmd1 Fitm2 Slc44a2 Nudt8 Phyh Pfkm Echs1 Ralgapa2 Kif26a Thrb Acadvl Mxi1 Jam3 Brp44 Sdhc

golgi apparatus protein 1 ornithine aminotransferase (gyrate atrophy) junctophilin 2 cytochrome c oxidase, subunit 8B pseudogene Src homology 2 domain containing E nuclear factor I/A KH domain containing, RNA binding, signal transduction associated 3 sphingosine-1-phosphate receptor 3 MAF1 homolog (S. cerevisiae) mitochondrial ribosomal protein S36 RIKEN cDNA 5930434B04 gene potassium inwardly-rectifying channel, subfamily J, member 8 lipin 1 RIKEN cDNA E130203B14 gene myosin, heavy chain 11, smooth muscle RIKEN cDNA 3110057O12 gene deformed epidermal autoregulatory factor 1 (Drosophila) tripartite motif-containing 63 enoyl-Coenzyme A, hydratase/3hydroxyacyl Coenzyme A dehydrogenase LSM domain containing 1 fat storage-inducing transmembrane protein 2 solute carrier family 44, member 2 nudix (nucleoside diphosphate linked moiety X)-type motif 8 phytanoyl-CoA 2-hydroxylase phosphofructokinase, muscle enoyl Coenzyme A hydratase, short chain, 1, mitochondrial Ral GTPase activating protein, alpha subunit 2 (catalytic) kinesin family member 26A thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian) acyl-Coenzyme A dehydrogenase, very long chain MAX interactor 1 junctional adhesion molecule 3 brain protein 44 succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa

53

-1.5

1.51E-04

-1.4

3.33E-04

-1.5 -1.4

1.12E-03 5.40E-03

-1.4 -1.4

1.68E-03 3.07E-03

-1.3 -1.4 -1.3

3.14E-04 2.27E-02 1.82E-02

-1.4 -1.4 -1.4

2.81E-05 1.32E-02 3.26E-03

-1.5 -1.5 -1.3 -1.4 -1.4

4.09E-03 1.70E-02 3.98E-02 1.59E-02 1.33E-02

-1.4 -1.4 -1.4 -1.4 -1.4

7.77E-03 1.97E-02 7.82E-03 1.06E-02 4.18E-03

-1.3 -1.3 -1.8 -1.4 -1.5

2.51E-02 8.90E-03 1.68E-03 7.98E-03 3.43E-03

-1.4 -1.4 -1.4 -1.4 -1.4

2.80E-03 6.36E-04 2.87E-02 2.50E-03 4.11E-03

-1.5 -1.4

1.39E-02 5.27E-03

-1.4 -1.4

1.53E-02 1.58E-03

-1.4 -1.4

3.19E-02 2.96E-03

-1.4 -1.4

1.60E-02 3.36E-04

-1.3 -1.6

5.75E-03 1.40E-03

-1.4 -1.4

5.44E-04 4.44E-03

-1.4 -1.4 -1.4

3.59E-02 4.33E-04 1.59E-03

-1.4 -1.4 -1.4

1.00E-02 5.17E-05 6.92E-04

-1.3

1.14E-02

-1.4

6.81E-04

-1.5 -1.3

1.08E-02 1.83E-02

-1.4 -1.4

1.07E-02 1.05E-03

-1.7

5.04E-03

-1.4

1.96E-02

-1.4 -1.5 -1.6 -1.6

1.24E-02 5.06E-04 1.29E-03 1.59E-04

-1.4 -1.4 -1.4 -1.4

1.82E-03 6.04E-04 3.48E-03 3.59E-04

-1.4

3.36E-03

-1.4

3.32E-04

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 54 of 70

54 Tecr Got2 Pqlc1 Asb10 Slc28a2 Thsd1 Sbk1 Sox18 Tmed1 Rilpl1 Suclg1 Hdlbp Actr3b Lpl Ndufs5 Pdlim7 Erc1 Acss1 Sdr39u1 Plekha5 Camk2n1 Lmf1 Gucy1a3 Tbx3 AI464131 Foxred1 Spsb1 6530418L21Rik Cars2 Itpr2 Npc1 Npc1

trans-2,3-enoyl-CoA reductase glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2) PQ loop repeat containing 1 ankyrin repeat and SOCS box-containing 10 solute carrier family 28 (sodiumcoupled nucleoside transporter), member 2 thrombospondin, type I, domain containing 1 SH3-binding domain kinase 1 SRY (sex determining region Y)-box 18 transmembrane emp24 protein transport domain containing 1 Rab interacting lysosomal protein-like 1 succinate-CoA ligase, alpha subunit high density lipoprotein binding protein (vigilin) ARP3 actin-related protein 3 homolog B (yeast) lipoprotein lipase NADH dehydrogenase (ubiquinone) Fe-S protein 5, 15kDa (NADH-coenzyme Q reductase) PDZ and LIM domain 7 (enigma) ELKS/RAB6-interacting/CAST family member 1 acyl-CoA synthetase short-chain family member 1 short chain dehydrogenase/reductase family 39U, member 1 pleckstrin homology domain containing, family A member 5 calcium/calmodulin-dependent protein kinase II inhibitor 1 lipase maturation factor 1 guanylate cyclase 1, soluble, alpha 3 T-box 3 (ulnar mammary syndrome) expressed sequence AI464131 FAD-dependent oxidoreductase domain containing 1 splA/ryanodine receptor domain and SOCS box containing 1 RIKEN cDNA 6530418L21 gene cysteinyl-tRNA synthetase 2, mitochondrial (putative) inositol 1,4,5-triphosphate receptor, type 2 Nasopharyngeal carcinoma 1 Niemann-Pick disease, type C1

54

-1.4

8.56E-03

-1.4

1.67E-03

-1.4 -1.4

1.21E-03 2.28E-03

-1.4 -1.4

3.46E-04 5.42E-04

-1.4

3.89E-03

-1.4

1.41E-03

-1.4

3.99E-02

-1.4

1.35E-02

-1.4 -1.5 -1.5

1.25E-03 2.81E-03 3.50E-02

-1.4 -1.4 -1.4

3.94E-04 2.16E-03 2.48E-02

-1.6 -1.5 -1.4

6.48E-05 6.25E-04 5.50E-03

-1.4 -1.4 -1.4

2.81E-04 2.04E-04 1.14E-03

-1.6

6.14E-06

-1.4

1.75E-05

-1.5 -1.5

3.15E-02 8.24E-04

-1.4 -1.4

3.46E-02 2.59E-04

-1.5 -1.8

7.39E-04 6.12E-04

-1.4 -1.4

2.74E-04 4.80E-03

-1.4

9.87E-06

-1.4

1.22E-06

-1.3

4.70E-02

-1.4

6.70E-03

-1.5

1.91E-03

-1.4

9.86E-04

-1.5

8.85E-03

-1.4

3.32E-03

-1.5 -1.6 -1.4 -1.6 -1.5

2.38E-02 4.31E-05 5.81E-03 5.73E-04 2.21E-02

-1.4 -1.5 -1.5 -1.5 -1.5

1.28E-02 1.65E-04 1.09E-03 6.81E-04 1.02E-02

-1.4

4.18E-03

-1.5

5.78E-04

-1.6 -1.9

1.52E-02 3.05E-03

-1.5 -1.5

2.03E-02 3.24E-02

-1.3

3.05E-02

-1.5

9.66E-04

-1.5 -1.4 -1.4

1.85E-02 2.99E-02 2.99E-02

-1.5 -1.5 -1.5

9.66E-03 2.60E-03 2.60E-03

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 55 of 70

55

Itgb1bp2 Cox7c Arl4d Kcna7 Klf9 Dbt Zfyve21 Pex6 Pde4d Mcc Mb Dcaf11 AI316807 G0s2 Atp5e Ipo13 Rasl10b Lrrc14b Npr1 Hdac5 Fbxo10 Rasal2 Hbb-b2 Slc25a4 Tnik Aga Hdac9 Gata2 Ndufab1 Hbb-b1 Hspa12b Lrtm1 Sh3rf2 Got2-ps1 Lrrc3b Hspa5

integrin beta 1 binding protein (melusin) 2 cytochrome c oxidase subunit VIIc ADP-ribosylation factor-like 4D potassium voltage-gated channel, shaker-related subfamily, member 7 Kruppel-like factor 9 dihydrolipoamide branched chain transacylase E2 zinc finger, FYVE domain containing 21 peroxisomal biogenesis factor 6 phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila) mutated in colorectal cancers myoglobin DDB1 and CUL4 associated factor 11 expressed sequence AI316807 G0/G1switch 2 ATP synthase, H transporting, mitochondrial F1 complex, epsilon subunit importin 13 RAS-like, family 10, member B leucine rich repeat containing 14B natriuretic peptide receptor A/guanylate cyclase A (atrionatriuretic peptide receptor A) histone deacetylase 5 F-box protein 10 RAS protein activator like 2 hemoglobin, beta adult minor chain solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4 TRAF2 and NCK interacting kinase aspartylglucosaminidase histone deacetylase 9 GATA binding protein 2 NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa hemoglobin, beta adult major chain heat shock 70kD protein 12B leucine-rich repeats and transmembrane domains 1 SH3 domain containing ring finger 2 glutamate oxaloacetate transaminase 2, mitochondrial, pseudogene 1 leucine rich repeat containing 3B heat shock 70kDa protein 5 (glucose-

55

-1.9 -1.3 -1.5

2.67E-06 1.00E-02 1.75E-02

-1.5 -1.5 -1.5

1.14E-04 3.26E-04 6.06E-03

-2.2 -1.5

1.44E-04 6.57E-03

-1.5 -1.5

1.10E-02 2.00E-03

-1.5 -1.3 -1.4

3.00E-03 1.23E-02 5.35E-03

-1.5 -1.5 -1.5

1.85E-03 2.56E-04 8.24E-04

-1.4 -1.4 -1.5 -1.3 -1.5 -1.7

4.55E-02 4.78E-02 9.84E-06 2.79E-02 3.70E-03 3.73E-03

-1.5 -1.5 -1.5 -1.5 -1.5 -1.5

6.56E-03 9.89E-03 1.72E-06 9.24E-04 6.97E-04 7.47E-03

-1.6 -2.3 -1.7 -1.7

4.72E-04 2.77E-06 3.12E-05 1.78E-05

-1.5 -1.5 -1.5 -1.5

8.98E-04 1.45E-03 1.27E-04 7.16E-05

-1.8 -1.4 -1.3 -1.9 -1.7

4.06E-03 1.44E-02 1.07E-02 7.71E-05 2.01E-02

-1.5 -1.5 -1.5 -1.5 -1.5

1.69E-02 8.59E-04 2.57E-04 1.77E-03 3.03E-02

-1.3 -1.7 -1.7 -1.4 -1.5

2.22E-03 6.06E-04 1.06E-02 2.43E-02 1.67E-02

-1.5 -1.5 -1.5 -1.5 -1.5

1.48E-05 1.67E-03 1.92E-02 2.59E-03 6.73E-03

-1.6 -1.7 -1.4

3.05E-03 3.49E-02 1.08E-02

-1.5 -1.5 -1.5

3.30E-03 4.61E-02 2.95E-04

-1.4 -1.4

2.23E-02 4.39E-02

-1.5 -1.5

3.18E-03 5.92E-03

-1.7 -2.4 -1.6

5.77E-04 2.54E-04 3.83E-02

-1.5 -1.5 -1.5

1.05E-03 1.87E-02 2.88E-02

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 56 of 70

56 regulated protein, 78kDa) Pcdh7 Slc25a11 Ache Ank1 1110031I02Rik Mut Det1 Rpl36-ps3 Nt5c1a Trip10 Icam2 Pla2g12a Slc9a3r2 Cacna2d1 6330403L08Rik Map4k2 Hey1 Btg1 U2af1l4 Myct1 Mlycd Gpr17 Osgepl1 Endog Phyhd1 BY080835 Fkbp4 Tfdp2 Bcl7a Pitpnc1 Iqcc Nod1 Abcb4 Scarf1

protocadherin 7 solute carrier family 25 (mitochondrial carrier; oxoglutarate carrier), member 11 acetylcholinesterase (Yt blood group) ankyrin 1, erythrocytic RIKEN cDNA 1110031I02 gene methylmalonyl Coenzyme A mutase de-etiolated homolog 1 (Arabidopsis) RP23-105M23.4 5'-nucleotidase, cytosolic IA thyroid hormone receptor interactor 10 intercellular adhesion molecule 2 phospholipase A2, group XIIA solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2 calcium channel, voltage-dependent, alpha 2/delta subunit 1 RIKEN cDNA 6330403L08 gene mitogen-activated protein kinase kinase kinase kinase 2 hairy/enhancer-of-split related with YRPW motif 1 B-cell translocation gene 1, antiproliferative U2 small nuclear RNA auxiliary factor 1like 4 myc target 1 malonyl-CoA decarboxylase G protein-coupled receptor 17 O-sialoglycoprotein endopeptidase-like 1 endonuclease G phytanoyl-CoA dioxygenase domain containing 1 cDNA sequence BY080835 FK506 binding protein 4, 59kDa transcription factor Dp-2 (E2F dimerization partner 2) B-cell CLL/lymphoma 7A phosphatidylinositol transfer protein, cytoplasmic 1 IQ motif containing C nucleotide-binding oligomerization domain containing 1 ATP-binding cassette, sub-family B (MDR/TAP), member 4 scavenger receptor class F, member 1

56

-1.4

1.45E-02

-1.5

3.49E-04

-1.3 -2.0 -1.3 -1.3 -1.5 -1.7 -1.7 -1.5 -1.3 -1.4 -1.4

1.90E-02 6.62E-03 2.83E-02 2.68E-02 1.78E-02 1.38E-02 1.95E-02 7.41E-03 3.62E-02 4.43E-02 3.68E-02

-1.5 -1.5 -1.5 -1.5 -1.5 -1.5 -1.5 -1.5 -1.5 -1.5 -1.6

2.69E-04 4.21E-02 3.60E-04 8.25E-04 7.00E-03 2.14E-02 2.88E-02 1.38E-03 5.86E-04 3.73E-03 5.60E-03

-1.3

2.56E-02

-1.6

6.28E-04

-2.0 -1.8

7.39E-05 1.96E-03

-1.6 -1.6

1.00E-03 4.16E-03

-1.4

3.29E-02

-1.6

1.24E-03

-1.9

1.20E-02

-1.6

3.41E-02

-1.5

2.10E-02

-1.6

3.87E-03

-1.3 -1.3 -1.3 -1.8

2.47E-02 3.76E-02 1.66E-02 2.61E-02

-1.6 -1.6 -1.6 -1.6

2.56E-04 7.68E-04 2.12E-04 3.55E-02

-1.4 -1.4

4.68E-02 3.35E-03

-1.6 -1.6

2.25E-03 6.79E-05

-2.0 -1.8 -1.4

9.11E-04 7.52E-04 3.35E-02

-1.6 -1.6 -1.6

6.27E-03 1.09E-03 1.13E-03

-1.7 -1.3

3.17E-04 1.33E-02

-1.6 -1.6

4.16E-04 4.78E-05

-1.7 -1.4

6.81E-03 4.21E-03

-1.6 -1.6

4.88E-03 1.19E-04

-1.7

1.49E-05

-1.6

1.69E-05

-1.6 -1.4

1.55E-03 3.23E-02

-1.6 -1.6

2.40E-04 9.90E-04

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 57 of 70

57

Cacna1c Hisppd1 Runx1t1 Ano1 Smtn Snrpn Macrod1 Lphn1 Msrb2 P2ry1 Fdft1 Ndufv3 Retsat Ccdc141 Mast2 Rit1 Pdk2 Gm9821 Gm14492 Abcb1a Bckdhb Lysmd4 2810025M15Rik Abhd8 Cmya5 Immp1l Art1 Slc46a3 Ppp1r3d Cmtm8 Abr Pdlim4 Stard13

calcium channel, voltage-dependent, L type, alpha 1C subunit histidine acid phosphatase domain containing 1 runt-related transcription factor 1; translocated to, 1 (cyclin D-related) anoctamin 1, calcium activated chloride channel smoothelin small nuclear ribonucleoprotein polypeptide N MACRO domain containing 1 latrophilin 1 methionine sulfoxide reductase B2 purinergic receptor P2Y, G-protein coupled, 1 farnesyl-diphosphate farnesyltransferase 1 NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa retinol saturase (all-trans-retinol 13,14reductase) coiled-coil domain containing 141 microtubule associated serine/threonine kinase 2 Ras-like without CAAX 1 pyruvate dehydrogenase kinase, isozyme 2 argininosuccinate synthase pseudogene 9821 predicted gene 14492 ATP-binding cassette, sub-family B (MDR/TAP), member 1A branched chain keto acid dehydrogenase E1, beta polypeptide (maple syrup urine disease) LysM, putative peptidoglycan-binding, domain containing 4 RIKEN cDNA 2810025M15 gene abhydrolase domain containing 8 cardiomyopathy associated 5 IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae) ADP-ribosyltransferase 1 solute carrier family 46, member 3 protein phosphatase 1, regulatory (inhibitor) subunit 3D CKLF-like MARVEL transmembrane domain containing 8 active BCR-related gene PDZ and LIM domain 4 StAR-related lipid transfer (START)

57

-1.4

5.52E-03

-1.6

1.14E-04

-1.7

6.60E-03

-1.6

4.85E-03

-2.3

3.10E-03

-1.6

3.61E-02

-1.5 -1.3

1.83E-02 1.35E-02

-1.6 -1.6

3.75E-03 2.82E-05

-2.1 -1.5 -1.7 -1.5

6.54E-08 1.61E-03 3.53E-02 2.74E-02

-1.6 -1.6 -1.6 -1.6

2.34E-06 1.03E-04 2.51E-02 1.95E-03

-1.5

1.16E-02

-1.6

7.00E-04

-1.5

9.28E-03

-1.6

5.86E-04

-1.4

5.46E-04

-1.6

2.41E-06

-1.6 -1.7

5.92E-03 9.39E-04

-1.6 -1.6

2.04E-03 6.11E-04

-1.4 -1.4

1.04E-03 4.49E-02

-1.6 -1.6

1.09E-05 1.00E-03

-1.3

5.34E-03

-1.7

8.28E-06

-1.5 -1.8

1.26E-02 1.24E-02

-1.7 -1.7

4.79E-04 9.20E-03

-1.9

6.02E-03

-1.7

1.05E-02

-1.9

1.42E-03

-1.7

2.10E-03

-1.6 -1.9 -1.4 -1.7

4.00E-04 1.68E-03 4.71E-02 3.36E-05

-1.7 -1.7 -1.7 -1.7

2.37E-05 3.01E-03 7.91E-04 1.13E-05

-2.3 -1.4 -1.6

2.04E-03 2.61E-02 3.30E-02

-1.7 -1.7 -1.7

1.61E-02 8.84E-04 1.15E-02

-1.7

6.75E-05

-1.7

1.33E-05

-1.7 -1.5 -1.5 -1.6

2.22E-02 8.67E-03 4.73E-02 1.16E-02

-1.7 -1.7 -1.7 -1.7

1.39E-02 2.23E-04 4.42E-03 1.33E-03

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 58 of 70

58

Nmnat3 Dut Atp2a2 Nr3c2 Trim68 Rxrg Pcnt Ncald Pink1 9330129D05Rik Klhdc1 Fam131a Cox4i2 2810432L12Rik 1810049H13Rik Etfb Yipf7 Mccc2 Pik3r1 Cobll1 Eepd1 Tesc Tnni3 Kcnj2 D830050J10Rik Aldh6a1 Atp8a1 Reep4 Pkia Ech1 Intu Trim7 Car14 Adamts7

domain containing 13 nicotinamide nucleotide adenylyltransferase 3 deoxyuridine triphosphatase ATPase, Ca transporting, cardiac muscle, slow twitch 2 nuclear receptor subfamily 3, group C, member 2 tripartite motif-containing 68 retinoid X receptor, gamma pericentrin neurocalcin delta PTEN induced putative kinase 1 acyl-Coenzyme A dehydrogenase family, member 12 kelch domain containing 1 family with sequence similarity 131, member A cytochrome c oxidase subunit IV isoform 2 (lung) RIKEN cDNA 2810432L12 gene RIKEN cDNA 1810049H13 gene electron-transfer-flavoprotein, beta polypeptide Yip1 domain family, member 7 methylcrotonoyl-Coenzyme A carboxylase 2 (beta) phosphoinositide-3-kinase, regulatory subunit 1 (alpha) COBL-like 1 endonuclease/exonuclease/phosphatase family domain containing 1 tescalcin troponin I type 3 (cardiac) potassium inwardly-rectifying channel, subfamily J, member 2 RIKEN cDNA D830050J10 gene aldehyde dehydrogenase 6 family, member A1 ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1 receptor accessory protein 4 protein kinase (cAMP-dependent, catalytic) inhibitor alpha enoyl Coenzyme A hydratase 1, peroxisomal inturned planar cell polarity effector homolog (Drosophila) tripartite motif-containing 7 carbonic anhydrase 14 ADAM metallopeptidase with

58

-1.7 -1.9

2.27E-02 1.31E-02

-1.7 -1.7

1.03E-02 1.52E-02

-1.5

1.71E-03

-1.7

3.17E-05

-1.8 -1.5 -1.6 -1.4 -2.4 -1.4

1.13E-02 3.04E-03 2.14E-03 2.12E-02 1.14E-04 7.39E-03

-1.7 -1.7 -1.7 -1.7 -1.7 -1.7

6.85E-03 5.24E-05 1.38E-04 1.10E-04 2.02E-03 4.84E-05

-1.3 -1.6

2.48E-02 9.53E-03

-1.7 -1.7

2.99E-05 8.47E-04

-1.5

9.49E-03

-1.7

3.64E-04

-2.3 -1.7 -1.5

1.63E-04 1.10E-02 2.28E-03

-1.7 -1.7 -1.7

1.87E-03 2.18E-03 3.91E-05

-1.6 -1.7

2.58E-04 3.19E-04

-1.7 -1.8

9.51E-06 6.25E-05

-1.5

5.70E-03

-1.8

8.50E-05

-1.5 -1.6

1.45E-02 5.66E-04

-1.8 -1.8

2.26E-04 1.97E-05

-1.9 -1.8 -1.4

6.57E-03 7.84E-05 1.69E-03

-1.8 -1.8 -1.8

3.94E-03 7.87E-06 1.16E-06

-1.8 -2.3

4.45E-03 3.93E-04

-1.8 -1.8

1.22E-03 2.04E-03

-1.5

1.78E-03

-1.8

8.57E-06

-1.8 -2.0

8.04E-03 8.03E-03

-1.8 -1.8

1.71E-03 6.00E-03

-2.6

1.99E-07

-1.8

7.53E-06

-1.5

3.07E-03

-1.8

1.82E-05

-1.8 -1.4 -1.6 -1.8

1.95E-03 2.89E-02 5.53E-03 5.24E-04

-1.8 -1.9 -1.9 -1.9

3.24E-04 1.39E-04 2.16E-04 4.95E-05

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 59 of 70

59 thrombospondin type 1 motif, 7 Hrc G630090E17Rik Asb15 Bcl2l12 Mmp15 Gzmm Pknox2 Ppm1k Pkig Ctsf Cox7a1 Syde2 Fitm1 Rpl3l 1700040L02Rik Ost4 Jph1 Cradd 5_8S_rRNA Asb18 Klhl38 Magix Aldh4a1 Selenbp1 Gpr155 2610528E23Rik 2010002N04Rik Dcakd 1110003O08Rik Pde4c Ung Fbxo31 Adra1b Phactr1 B9d2

histidine rich calcium binding protein RIKEN cDNA G630090E17 gene ankyrin repeat and SOCS box-containing 15 BCL2-like 12 (proline rich) matrix metallopeptidase 15 (membraneinserted) granzyme M (lymphocyte met-ase 1) PBX/knotted 1 homeobox 2 protein phosphatase 1K (PP2C domain containing) protein kinase (cAMP-dependent, catalytic) inhibitor gamma cathepsin F cytochrome c oxidase subunit VIIa polypeptide 1 (muscle) synapse defective 1, Rho GTPase, homolog 2 (C. elegans) fat storage-inducing transmembrane protein 1 ribosomal protein L3-like RIKEN cDNA 1700040L02 gene oligosaccharyltransferase 4 homolog (S. cerevisiae) junctophilin 1 CASP2 and RIPK1 domain containing adaptor with death domain 5.8S ribosomal RNA ankyrin repeat and SOCS box-containing 18 kelch-like 38 (Drosophila) MAGI family member, X-linked aldehyde dehydrogenase 4 family, member A1 selenium binding protein 1 G protein-coupled receptor 155 RIKEN cDNA 2610528E23 gene RIKEN cDNA 2010002N04 gene dephospho-CoA kinase domain containing RIKEN cDNA 1110003O08 gene phosphodiesterase 4C, cAMP-specific (phosphodiesterase E1 dunce homolog, Drosophila) uracil-DNA glycosylase F-box protein 31 adrenergic, alpha-1B-, receptor phosphatase and actin regulator 1 B9 protein domain 2

59

-1.3 -2.9

1.25E-02 1.97E-04

-1.9 -1.9

8.38E-07 5.01E-03

-1.9 -2.0

2.36E-04 2.16E-03

-1.9 -1.9

5.69E-05 1.35E-03

-1.6 -1.7 -2.1

1.69E-03 6.69E-03 4.99E-03

-1.9 -1.9 -1.9

1.17E-05 3.16E-04 4.65E-03

-1.5

2.02E-02

-1.9

9.45E-05

-1.5 -1.5

7.61E-04 3.18E-02

-1.9 -1.9

6.01E-07 6.00E-04

-1.8

4.53E-07

-1.9

1.66E-08

-2.1

5.71E-04

-1.9

5.33E-04

-1.5 -1.7 -2.0

8.05E-03 3.41E-04 4.78E-03

-1.9 -1.9 -1.9

1.54E-05 7.31E-06 2.51E-03

-2.0 -1.7

2.58E-02 1.67E-03

-2.0 -2.0

1.35E-02 2.87E-05

-1.6 -3.5

3.90E-02 8.09E-04

-2.0 -2.0

1.66E-03 1.68E-02

-1.7 -1.8 -1.7

4.39E-03 6.03E-03 2.25E-03

-2.0 -2.0 -2.0

9.32E-05 5.59E-04 6.04E-05

-1.4 -1.4 -2.2 -1.7 -2.6

5.53E-03 1.97E-02 9.11E-03 4.40E-03 1.85E-04

-2.0 -2.0 -2.0 -2.0 -2.0

1.71E-06 6.94E-06 6.14E-03 5.85E-05 6.86E-04

-2.2 -2.0

3.66E-06 2.29E-03

-2.0 -2.0

2.39E-06 4.00E-04

-1.9 -1.8 -1.7 -1.8 -1.6 -1.5

3.49E-02 1.02E-02 1.34E-05 2.34E-03 4.78E-02 4.16E-02

-2.1 -2.1 -2.1 -2.1 -2.1 -2.1

6.58E-03 4.44E-04 2.71E-08 7.93E-05 9.96E-04 4.10E-04

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 60 of 70

60 Arhgap20 Fam65b Cyp4b1 Slc25a34 Tnfaip8 Pla2g4e Klf15 Igf2 Syt7 Corin Lrg1 Grb14 Tmem82 Chd6 Asb4 Pdp2 Slc26a10 Ldhd Dgat2 Gstm7 Csdc2 Cdkn1c Rtn2 Pxmp2 D9Ertd402e U1 Slc22a3 Cd59b SNORA55 Sema6c Aspdh Sned1 Thbs2 Cpn2

Rho GTPase activating protein 20 family with sequence similarity 65, member B cytochrome P450, family 4, subfamily B, polypeptide 1 solute carrier family 25, member 34 tumor necrosis factor, alpha-induced protein 8 phospholipase A2, group IVE Kruppel-like factor 15 insulin-like growth factor 2 (somatomedin A) synaptotagmin VII corin, serine peptidase leucine-rich alpha-2-glycoprotein 1 growth factor receptor-bound protein 14 transmembrane protein 82 chromodomain helicase DNA binding protein 6 ankyrin repeat and SOCS box-containing 4 pyruvate dehydrogenase phosphatase isoenzyme 2 solute carrier family 26, member 10 lactate dehydrogenase D diacylglycerol O-acyltransferase homolog 2 (mouse) glutathione S-transferase, mu 7 cold shock domain containing C2, RNA binding cyclin-dependent kinase inhibitor 1C (p57, Kip2) reticulon 2 peroxisomal membrane protein 2, 22kDa DNA segment, Chr 9, ERATO Doi 402, expressed U1 small nuclear ribonucleoprotein solute carrier family 22 (extraneuronal monoamine transporter), member 3 CD59b antigen small nucleolar RNA, H/ACA box 55 sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C aspartate dehydrogenase domain containing sushi, nidogen and EGF-like domains 1 thrombospondin 2 carboxypeptidase N, polypeptide 2

60

-1.9

1.02E-04

-2.1

3.17E-06

-1.6

3.66E-02

-2.1

9.01E-04

-2.1 -1.6

2.38E-03 8.39E-03

-2.1 -2.1

6.45E-04 2.01E-05

-1.6 -1.8 -1.7

2.50E-02 2.50E-02 1.08E-02

-2.2 -2.2 -2.2

3.61E-04 1.16E-03 7.75E-05

-1.8 -1.7 -1.6 -1.5

1.01E-02 1.33E-02 4.80E-03 1.28E-02

-2.2 -2.2 -2.2 -2.2

2.59E-04 1.93E-04 5.09E-06 7.35E-06

-2.3 -2.3

3.09E-08 3.75E-03

-2.2 -2.2

4.59E-09 1.66E-03

-3.0

1.90E-03

-2.3

4.24E-03

-2.5

2.77E-02

-2.3

1.91E-02

-1.7 -1.3 -1.6

1.43E-03 4.51E-02 4.97E-03

-2.3 -2.3 -2.3

1.45E-06 8.59E-07 1.75E-06

-1.7 -1.6

3.84E-03 3.78E-03

-2.3 -2.3

1.62E-05 1.93E-06

-2.1

7.70E-05

-2.4

2.30E-06

-1.7 -2.0

7.12E-03 3.10E-04

-2.4 -2.4

2.13E-05 5.17E-06

-1.3

4.51E-02

-2.5

2.17E-07

-2.0 -2.2

4.56E-04 3.77E-02

-2.5 -2.5

5.02E-06 6.89E-03

-2.2 -2.3 -3.6

3.96E-04 3.35E-02 2.05E-02

-2.6 -2.6 -2.6

1.01E-05 5.94E-03 3.87E-02

-3.4

1.03E-03

-2.6

1.85E-03

-2.8 -1.8 -1.6 -1.7

3.04E-02 4.97E-03 3.60E-02 2.70E-02

-2.7 -2.7 -2.8 -2.8

1.45E-02 7.59E-06 3.51E-05 4.04E-05

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 61 of 70

61 Il15 Dusp23 Dhrs7c Ano10 Mboat2 mmu-mir-208b Fah Gpt Art4 Mrgprh 9030617O03Rik Acsl6 Cadm4 Lgals4 H19 Gcat A530016L24Rik Lrrc4b Art5 Rps6ka2 mmu-mir-21343 Mpped2 Angpt1 Gstk1 3632451O06Rik Clcn1 Efnb3 1700088E04Rik Wnk2 Asb14 Hcn4 A2bp1 Pla2g5 Kcnd2 Ogdhl

interleukin 15 dual specificity phosphatase 23 dehydrogenase/reductase (SDR family) member 7C anoctamin 10 membrane bound O-acyltransferase domain containing 2 mmu-mir-208b fumarylacetoacetate hydrolase (fumarylacetoacetase) glutamic-pyruvate transaminase (alanine aminotransferase) ADP-ribosyltransferase 4 (Dombrock blood group) MAS-related GPR, member H RIKEN cDNA 9030617O03 gene acyl-CoA synthetase long-chain family member 6 cell adhesion molecule 4 lectin, galactoside-binding, soluble, 4 (galectin 4) H19, imprinted maternally expressed transcript (non-protein coding) glycine C-acetyltransferase (2-amino-3ketobutyrate coenzyme A ligase) RIKEN cDNA A530016L24 gene leucine rich repeat containing 4B ADP-ribosyltransferase 5 ribosomal protein S6 kinase, 90kDa, polypeptide 2

-3.4 -2.2

7.20E-04 2.59E-03

-2.8 -2.8

8.33E-04 6.42E-05

-3.3 -2.1

4.82E-08 3.27E-05

-2.8 -2.9

3.56E-08 4.54E-08

-3.0 -2.3

7.06E-05 9.58E-03

-2.9 -2.9

1.75E-05 4.46E-04

-2.0

2.76E-04

-3.0

1.67E-07

-1.7

1.68E-03

-3.0

6.82E-08

-2.0 -3.6 -2.3

1.56E-03 6.37E-05 4.87E-05

-3.0 -3.0 -3.0

4.17E-06 5.67E-05 2.22E-07

-3.3 -1.9

5.90E-03 8.68E-04

-3.1 -3.1

2.76E-03 3.50E-07

-1.8

6.53E-03

-3.1

3.37E-06

-3.3

8.62E-03

-3.2

3.68E-03

-2.0 -1.7 -2.0 -2.1

1.72E-03 9.23E-03 4.21E-03 2.98E-03

-3.2 -3.2 -3.3 -3.4

1.50E-06 5.16E-07 7.05E-06 5.11E-06

-2.2

5.22E-05

-3.4

3.65E-08

mmu-mir-2134-3 metallophosphoesterase domain containing 2 angiopoietin 1 glutathione S-transferase kappa 1 RIKEN cDNA 3632451O06 gene chloride channel 1, skeletal muscle (Thomsen disease, autosomal dominant) ephrin-B3 RIKEN cDNA 1700088E04 gene WNK lysine deficient protein kinase 2 ankyrin repeat and SOCS box-containing 14 hyperpolarization activated cyclic nucleotide-gated potassium channel 4 ataxin 2-binding protein 1 phospholipase A2, group V potassium voltage-gated channel, Shalrelated subfamily, member 2 oxoglutarate dehydrogenase-like

-2.3

2.22E-02

-3.4

3.97E-04

-2.2 -2.4 -2.5 -2.5

2.06E-02 1.38E-02 1.81E-07 7.15E-03

-3.4 -3.5 -3.6 -3.6

2.53E-04 2.46E-04 2.12E-10 9.51E-05

-2.3 -2.6 -5.5 -2.1

1.53E-03 4.56E-05 2.12E-02 6.71E-04

-3.8 -4.0 -4.0 -4.1

2.90E-06 8.53E-08 2.77E-02 4.88E-08

-6.4

9.16E-09

-4.2

3.93E-08

-2.9 -2.4 -3.6

1.96E-03 5.25E-05 4.70E-03

-4.2 -4.2 -4.3

3.08E-05 1.27E-08 4.94E-04

-3.4 -3.7

1.85E-05 2.32E-05

-4.6 -4.6

1.53E-07 5.22E-07

61

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 62 of 70

62 Armc2 Maob Asb5 Dbh Ptprn2 Ttll1 Myl1 Acot1 Pcp4l1 Mfn2 Cenpf Gfra4 Hcn1 Rhbdl3 Phkg1 Cacna1s 2310010M20Rik Pfkfb1

armadillo repeat containing 2 monoamine oxidase B ankyrin repeat and SOCS box-containing 5 dopamine beta-hydroxylase (dopamine beta-monooxygenase) protein tyrosine phosphatase, receptor type, N polypeptide 2 tubulin tyrosine ligase-like family, member 1 myosin, light chain 1, alkali; skeletal, fast acyl-CoA thioesterase 1 Purkinje cell protein 4 like 1 mitofusin 2 centromere protein F, 350/400ka (mitosin) GDNF family receptor alpha 4 hyperpolarization activated cyclic nucleotide-gated potassium channel 1 rhomboid, veinlet-like 3 (Drosophila) phosphorylase kinase, gamma 1 (muscle) calcium channel, voltage-dependent, L type, alpha 1S subunit RIKEN cDNA 2310010M20 gene 6-phosphofructo-2-kinase/fructose-2,6biphosphatase 1

62

-3.2 -5.3

1.64E-06 1.35E-06

-4.6 -4.7

4.56E-09 5.41E-07

-5.4

5.77E-06

-4.8

1.99E-06

-7.8

2.73E-06

-4.9

1.79E-05

-2.9

1.93E-05

-4.9

1.74E-08

-3.4 -4.6 -3.7 -3.1 -7.1

6.35E-10 7.30E-05 1.32E-02 1.42E-06 6.99E-11

-5.0 -5.1 -5.1 -5.4 -5.7

9.54E-13 6.72E-06 9.86E-04 7.47E-10 4.02E-11

-3.9 -2.9

1.24E-03 1.55E-03

-6.1 -6.7

1.72E-05 6.98E-07

-8.5 -4.0

1.85E-04 5.09E-09

-6.9 -7.2

1.11E-04 2.67E-12

-6.1

3.17E-06

-7.2

1.46E-07

-4.9 -5.9

8.85E-03 2.47E-06

-10.6 -12.9

2.25E-05 2.05E-09

-5.3

2.59E-04

-16.7

2.65E-07

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 63 of 70

63 Supplemental Table 2. Relative expression (vs control) of 183 nuclear-encoded mitochondrial genes regulated in Mfn2-deficient hearts. Results are plotted in descending order of regulation in 16 week Mfn2 KO.

Gene Symbol

6wk fold change

Gene name

6 wk p-value

16wk fold change

16 wk p-value

MTHFD2

methylenetetrahydrofolate dehydrogenase (NADP dependent) 2, methenyltetrahydrofolate cyclohydrolase

11.9

1.33E-07

24.9

3.58E-10

UQCRB BCL2 ACSF2 PYCR1

ubiquinol-cytochrome c reductase binding protein B-cell CLL/lymphoma 2 acyl-CoA synthetase family member 2 pyrroline-5-carboxylate reductase 1

1.0 3.1 4.1 2.5

8.89E-01 5.06E-07 2.07E-08 9.24E-03

4.0 3.9 3.0 3.0

6.91E-05 5.28E-09 7.03E-08 6.96E-04

UCP2

uncoupling protein 2 (mitochondrial, proton carrier)

2.7

9.36E-06

2.9

6.30E-07

ACSL3

acyl-CoA synthetase long-chain family member 3

1.5

1.28E-01

2.8

3.62E-04

ALDH18A1

aldehyde dehydrogenase 18 family, member A1

1.4

1.75E-01

2.7

3.01E-04

ABCE1 GPX1 MTX2

ATP-binding cassette, sub-family E (OABP), member 1 glutathione peroxidase 1 metaxin 2

1.1 2.3 -1.1

5.89E-01 7.10E-06 6.94E-01

2.3 2.3 2.3

5.93E-05 9.10E-07 7.05E-04

CASQ1

calsequestrin 1 (fast-twitch, skeletal muscle)

2.2

3.10E-02

2.3

1.30E-02

CMC1 TFAM GLS

COX assembly mitochondrial protein homolog (S. cerevisiae) transcription factor A, mitochondrial glutaminase

1.3 1.2 1.0

2.39E-01 4.33E-01 9.57E-01

2.2 2.1 2.1

1.77E-03 1.80E-03 3.19E-04

NDUFB4

NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15kDa

1.2

3.14E-01

2.0

1.82E-04

ME2

malic enzyme 2, NAD()-dependent, mitochondrial

1.9

7.51E-04

1.9

2.27E-04

FAM82A2 LRRK2 TSPO

family with sequence similarity 82, member A2 leucine-rich repeat kinase 2 translocator protein (18kDa)

1.3 1.3 1.7

6.31E-02 1.24E-01 2.79E-03

1.9 1.9 1.8

1.10E-04 1.86E-04 1.39E-04

NLN MRPS18B GSR

neurolysin (metallopeptidase M3 family) mitochondrial ribosomal protein S18B glutathione reductase

1.3 1.3 1.5

2.13E-01 6.65E-02 6.89E-03

1.8 1.8 1.8

8.91E-04 2.24E-04 7.82E-05

63

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

64Page 64 of 70

ALDH1B1

aldehyde dehydrogenase 1 family, member B1

3.2

2.91E-05

1.8

3.65E-03

SLC25A5 MRPL20 SLC25A33

solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5 mitochondrial ribosomal protein L20 solute carrier family 25, member 33

1.4 1.2 1.1

3.70E-03 2.94E-01 5.61E-01

1.8 1.7 1.7

1.21E-05 9.75E-04 6.72E-03

REXO2 HSPA9

REX2, RNA exonuclease 2 homolog (S. cerevisiae) heat shock 70kDa protein 9 (mortalin)

1.5 1.2

1.74E-02 2.13E-01

1.7 1.7

1.37E-03 3.32E-04

TIMM10

translocase of inner mitochondrial membrane 10 homolog (yeast)

1.7

3.29E-05

1.7

1.51E-05

TOMM70A

translocase of outer mitochondrial membrane 70 homolog A (S. cerevisiae)

1.2

1.45E-01

1.7

8.45E-05

COX8A GRPEL2 GLRX2

cytochrome c oxidase subunit 8A (ubiquitous) GrpE-like 2, mitochondrial (E. coli) glutaredoxin 2

1.4 1.4 1.2

3.09E-03 1.08E-01 1.40E-01

1.6 1.6 1.6

1.21E-05 7.99E-03 9.45E-04

SH3BP5

SH3-domain binding protein 5 (BTKassociated)

1.8

1.46E-03

1.6

2.88E-03

ACBD3 GLOD4

acyl-Coenzyme A binding domain containing 3 glyoxalase domain containing 4

1.2 1.3

6.46E-02 2.17E-01

1.6 1.6

1.36E-04 7.01E-03

RSAD1 HK1

radical S-adenosyl methionine domain containing 1 hexokinase 1

1.1 1.4

5.72E-01 2.36E-04

1.6 1.6

6.75E-03 4.46E-06

SCO1

SCO cytochrome oxidase deficient homolog 1 (yeast)

1.2

4.34E-01

1.6

1.48E-02

TIMM9 AMT

translocase of inner mitochondrial membrane 9 homolog (yeast) aminomethyltransferase

1.6 1.1

2.30E-02 4.46E-01

1.6 1.6

1.37E-02 6.38E-03

CYP27A1 PRELID1 MRPS6

cytochrome P450, family 27, subfamily A, polypeptide 1 PRELI domain containing 1 mitochondrial ribosomal protein S6

1.4 1.2 1.2

7.12E-02 1.69E-01 2.61E-01

1.5 1.5 1.5

9.39E-03 4.82E-04 6.28E-03

RNASEL MFF VDAC2 BCL2L2 MRPL32 FDX1L MSTO1

ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent) mitochondrial fission factor voltage-dependent anion channel 2 BCL2-like 2 mitochondrial ribosomal protein L32 ferredoxin 1-like misato homolog 1 (Drosophila)

1.5 1.1 1.0 1.1 1.2 1.1 1.3

4.13E-02 3.48E-01 9.20E-01 4.65E-01 2.64E-01 5.75E-01 4.97E-02

1.5 1.4 1.4 1.4 1.4 1.4 1.4

3.27E-02 8.06E-03 1.34E-03 9.99E-06 3.35E-02 2.61E-03 4.52E-03

64

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 65 of 70

65

COX6A1 ATPIF1 CYB5R3 LONP1 MRPL53

cytochrome c oxidase subunit VIa polypeptide 1 ATPase inhibitory factor 1 cytochrome b5 reductase 3 lon peptidase 1, mitochondrial mitochondrial ribosomal protein L53

1.3 1.6 1.4 1.4 1.0

2.53E-02 1.98E-04 4.69E-03 5.48E-03 9.55E-01

1.4 1.4 1.4 1.4 1.4

1.67E-03 1.48E-03 1.40E-03 1.39E-03 1.77E-03

GPX4 SLC25A37 MRPS23

glutathione peroxidase 4 (phospholipid hydroperoxidase) solute carrier family 25, member 37 mitochondrial ribosomal protein S23

1.6 2.1 1.6

1.64E-04 1.93E-05 1.34E-04

1.4 1.4 1.4

1.71E-03 9.43E-03 2.12E-03

RAB11FIP5 MRPL16 MRPS2

RAB11 family interacting protein 5 (class I) mitochondrial ribosomal protein L16 mitochondrial ribosomal protein S2

1.3 1.2 1.2

8.81E-03 1.04E-01 2.10E-01

1.4 1.3 1.3

5.96E-04 7.30E-03 2.18E-02

SLC25A23

solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23

1.5

9.08E-04

1.3

5.44E-03

ARL2BP

ADP-ribosylation factor-like 2 binding protein

1.2

9.20E-02

1.3

1.27E-03

MCL1

myeloid cell leukemia sequence 1 (BCL2-related)

1.1

5.08E-01

1.3

4.23E-03

ACAD9

acyl-Coenzyme A dehydrogenase family, member 9

1.2

2.71E-01

1.3

3.35E-02

PGS1 AK2 MRPL18

phosphatidylglycerophosphate synthase 1 adenylate kinase 2 mitochondrial ribosomal protein L18

1.1 1.3 -1.1

6.12E-01 2.50E-03 3.27E-01

1.3 1.3 -1.3

4.06E-03 1.87E-03 2.76E-02

AGXT2L2

alanine-glyoxylate aminotransferase 2like 2

-1.1

3.67E-01

-1.3

4.07E-02

ACSL1

acyl-CoA synthetase long-chain family member 1

-1.3

3.23E-03

-1.3

5.77E-03

HSD17B10

hydroxysteroid (17-beta) dehydrogenase 10

-1.3

6.17E-02

-1.3

2.78E-02

ATP5J2

ATP synthase, H transporting, mitochondrial F0 complex, subunit F2

-1.3

5.81E-03

-1.3

5.49E-03

METT11D1 OXA1L

methyltransferase 11 domain containing 1 oxidase (cytochrome c) assembly 1-like

-1.4 -1.1

1.60E-02 2.16E-01

-1.3 -1.3

3.80E-02 9.49E-04

NDUFA13

NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13

-1.1

9.83E-02

-1.3

1.72E-03

FIS1

fission 1 (mitochondrial outer membrane) homolog (S. cerevisiae)

-1.2

9.76E-02

-1.3

7.58E-03

ATP5A1

ATP synthase, H transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle

-1.1

2.05E-01

-1.3

7.24E-03

65

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

66

Page 66 of 70

NDUFS2

NADH dehydrogenase (ubiquinone) FeS protein 2, 49kDa (NADH-coenzyme Q reductase)

-1.2

3.28E-02

-1.3

5.43E-04

ATP5G3 GBAS

ATP synthase, H transporting, mitochondrial F0 complex, subunit C3 (subunit 9) glioblastoma amplified sequence

-1.2 -1.2

6.60E-02 1.01E-01

-1.3 -1.3

2.27E-03 4.16E-03

NDUFB3

NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3, 12kDa

-1.2

1.32E-01

-1.3

8.88E-03

SDHB

succinate dehydrogenase complex, subunit B, iron sulfur (Ip)

-1.3

1.77E-02

-1.3

2.35E-03

NDUFC2

NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2, 14.5kDa

-1.3

2.23E-02

-1.3

4.15E-03

COQ10A

coenzyme Q10 homolog A (S. cerevisiae)

-1.2

7.86E-02

-1.3

1.39E-02

NDUFB6

NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa

-1.1

3.23E-01

-1.3

2.21E-02

NDUFS8

NADH dehydrogenase (ubiquinone) FeS protein 8, 23kDa (NADH-coenzyme Q reductase)

-1.2

3.81E-02

-1.3

2.88E-03

NDUFA3 IDH3B COX6C RHOT2

NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3, 9kDa isocitrate dehydrogenase 3 (NAD) beta cytochrome c oxidase subunit VIc ras homolog gene family, member T2

-1.3 -1.1 -1.4 -1.1

9.96E-02 9.10E-02 1.56E-03 3.97E-01

-1.3 -1.3 -1.3 -1.3

2.45E-02 5.07E-04 1.06E-03 2.79E-03

UQCRQ

ubiquinol-cytochrome c reductase, complex III subunit VII, 9.5kDa

-1.2

9.25E-02

-1.3

1.70E-03

IDH2 SLC25A26

isocitrate dehydrogenase 2 (NADP), mitochondrial solute carrier family 25, member 26

-1.0 -1.5

9.14E-01 1.09E-03

-1.3 -1.3

3.70E-03 5.87E-03

UQCRC1

ubiquinol-cytochrome c reductase core protein I

-1.2

1.53E-01

-1.3

3.26E-03

COQ2

coenzyme Q2 homolog, prenyltransferase (yeast)

-1.2

1.56E-01

-1.3

2.85E-03

TST

thiosulfate sulfurtransferase (rhodanese)

-1.2

2.21E-01

-1.3

3.15E-02

NDUFB11

NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11, 17.3kDa

-1.1

1.76E-01

-1.3

2.98E-03

NDUFV1

NADH dehydrogenase (ubiquinone) flavoprotein 1, 51kDa

-1.2

8.90E-02

-1.3

1.36E-03

BCAT2 MRPL28

branched chain aminotransferase 2, mitochondrial mitochondrial ribosomal protein L28

-1.1 -1.3

1.90E-01 8.74E-03

-1.3 -1.3

7.26E-04 3.01E-04

NDUFA2

NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa

-1.4

6.27E-03

-1.4

2.46E-03

66

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 67 of 70

67 MRPL27

mitochondrial ribosomal protein L27

-1.5

5.62E-03

-1.4

8.66E-03

TOMM40L

translocase of outer mitochondrial membrane 40 homolog (yeast)-like

-1.4

8.38E-03

-1.4

4.21E-03

PCCB CRAT

propionyl Coenzyme A carboxylase, beta polypeptide carnitine acetyltransferase

-1.0 -1.0

7.86E-01 8.73E-01

-1.4 -1.4

4.24E-03 7.15E-03

OAT

ornithine aminotransferase (gyrate atrophy)

-1.5

1.12E-03

-1.4

1.68E-03

SLC25A12

solute carrier family 25 (mitochondrial carrier, Aralar), member 12

-1.2

1.63E-01

-1.4

3.02E-03

NNT

nicotinamide nucleotide transhydrogenase

-1.2

1.64E-01

-1.4

5.25E-03

ACADS MRPS36

acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain mitochondrial ribosomal protein S36

-1.2 -1.4

8.39E-02 1.59E-02

-1.4 -1.4

1.40E-03 1.06E-02

NDUFA1

NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1, 7.5kDa

-1.2

6.57E-03

-1.4

2.48E-06

ISCU

iron-sulfur cluster scaffold homolog (E. coli)

-1.3

4.02E-02

-1.4

1.88E-03

NDUFS6

NADH dehydrogenase (ubiquinone) FeS protein 6, 13kDa (NADH-coenzyme Q reductase)

-1.1

3.01E-01

-1.4

5.20E-04

NUDT8

nudix (nucleoside diphosphate linked moiety X)-type motif 8

-1.4

3.59E-02

-1.4

1.00E-02

ECHS1

enoyl Coenzyme A hydratase, short chain, 1, mitochondrial

-1.3

1.14E-02

-1.4

6.81E-04

ACADVL

acyl-Coenzyme A dehydrogenase, very long chain

-1.4

1.24E-02

-1.4

1.82E-03

NDUFS7

NADH dehydrogenase (ubiquinone) FeS protein 7, 20kDa (NADH-coenzyme Q reductase)

-1.2

1.04E-01

-1.4

8.50E-04

SDHC COQ9

succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa coenzyme Q9 homolog (S. cerevisiae)

-1.4 -1.2

3.36E-03 8.30E-02

-1.4 -1.4

3.32E-04 1.32E-04

GOT2 SLC25A29 SUCLG1

glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2) solute carrier family 25, member 29 succinate-CoA ligase, alpha subunit

-1.4 -1.3 -1.4

1.21E-03 1.60E-01 5.50E-03

-1.4 -1.4 -1.4

3.46E-04 4.56E-02 1.14E-03

MPV17

MpV17 mitochondrial inner membrane protein

-1.3

3.07E-02

-1.4

4.97E-04

NDUFS5

NADH dehydrogenase (ubiquinone) FeS protein 5, 15kDa (NADH-coenzyme Q reductase)

-1.5

7.39E-04

-1.4

2.74E-04

67

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

68Page 68 of 70

ACSS1

acyl-CoA synthetase short-chain family member 1

-1.3

4.70E-02

-1.4

6.70E-03

ACADM

acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain

-1.1

1.95E-01

-1.5

2.17E-04

UQCR

ubiquinol-cytochrome c reductase, 6.4kDa subunit

-1.0

5.44E-01

-1.5

4.23E-07

CARS2 COX7C

cysteinyl-tRNA synthetase 2, mitochondrial (putative) cytochrome c oxidase subunit VIIc

-1.3 -1.3

3.05E-02 1.00E-02

-1.5 -1.5

9.66E-04 3.26E-04

DBT

dihydrolipoamide branched chain transacylase E2

-1.5

3.00E-03

-1.5

1.85E-03

ATP5E

ATP synthase, H transporting, mitochondrial F1 complex, epsilon subunit

-1.6

4.72E-04

-1.5

8.98E-04

SLC25A4

solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4

-1.3

2.22E-03

-1.5

1.48E-05

ECHDC3

enoyl Coenzyme A hydratase domain containing 3

-1.0

8.75E-01

-1.5

3.83E-03

NDUFAB1

NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa

-1.6

3.05E-03

-1.5

3.30E-03

SLC25A11 MUT

solute carrier family 25 (mitochondrial carrier; oxoglutarate carrier), member 11 methylmalonyl Coenzyme A mutase

-1.3 -1.5

1.90E-02 1.78E-02

-1.5 -1.5

2.69E-04 7.00E-03

CABC1

chaperone, ABC1 activity of bc1 complex homolog (S. pombe)

-1.3

6.23E-02

-1.5

6.44E-04

ALDH2

aldehyde dehydrogenase 2 family (mitochondrial)

-1.3

7.31E-02

-1.5

2.28E-03

COX6A2 ACAA2 MLYCD MPST IVD ENDOG

cytochrome c oxidase subunit VIa polypeptide 2 acetyl-Coenzyme A acyltransferase 2 malonyl-CoA decarboxylase mercaptopyruvate sulfurtransferase isovaleryl Coenzyme A dehydrogenase endonuclease G

-1.1 -1.3 -1.3 -1.2 -1.2 -1.4

3.00E-01 7.11E-02 1.66E-02 2.76E-01 5.95E-02 3.35E-03

-1.6 -1.6 -1.6 -1.6 -1.6 -1.6

9.49E-06 1.61E-03 2.12E-04 5.83E-03 1.18E-04 6.79E-05

ETFDH PRODH MSRB2 TMEM143

electron-transferring-flavoprotein dehydrogenase proline dehydrogenase (oxidase) 1 methionine sulfoxide reductase B2 transmembrane protein 143

-1.2 -1.3 -1.5 -1.3

1.58E-01 3.25E-01 2.74E-02 4.85E-02

-1.6 -1.6 -1.6 -1.6

4.17E-04 2.31E-02 1.95E-03 8.20E-05

NDUFV3

NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa

-1.4

5.46E-04

-1.6

2.41E-06

PDK2

pyruvate dehydrogenase kinase, isozyme 2

-1.3

5.34E-03

-1.7

8.28E-06

68

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

69

Page 69 of 70

BCKDHB SLC25A42

branched chain keto acid dehydrogenase E1, beta polypeptide (maple syrup urine disease) solute carrier family 25, member 42

-1.9 -1.1

1.42E-03 2.03E-01

-1.7 -1.7

2.10E-03 2.88E-06

IMMP1L

IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)

-2.3

2.04E-03

-1.7

1.61E-02

ADHFE1

alcohol dehydrogenase, iron containing, 1

-1.1

7.20E-01

-1.7

1.20E-03

STARD13 SQRDL DUT

StAR-related lipid transfer (START) domain containing 13 sulfide quinone reductase-like (yeast) deoxyuridine triphosphatase

-1.6 -1.3 -1.9

1.16E-02 6.89E-02 1.31E-02

-1.7 -1.7 -1.7

1.33E-03 6.58E-04 1.52E-02

MMAB PINK1

methylmalonic aciduria (cobalamin deficiency) cblB type PTEN induced putative kinase 1

-1.1 -1.4

5.10E-01 7.39E-03

-1.7 -1.7

1.32E-04 4.84E-05

COX4I2

cytochrome c oxidase subunit IV isoform 2 (lung)

-2.3

1.63E-04

-1.7

1.87E-03

ETFB

electron-transfer-flavoprotein, beta polypeptide

-1.6

2.58E-04

-1.7

9.51E-06

MCCC2 ABAT

methylcrotonoyl-Coenzyme A carboxylase 2 (beta) 4-aminobutyrate aminotransferase

-1.5 1.0

5.70E-03 8.45E-01

-1.8 -1.8

8.50E-05 6.56E-04

ALDH6A1

aldehyde dehydrogenase 6 family, member A1

-1.5

1.78E-03

-1.8

8.57E-06

ECH1

enoyl Coenzyme A hydratase 1, peroxisomal

-1.5

3.07E-03

-1.8

1.82E-05

PPM1K

protein phosphatase 1K (PP2C domain containing)

-1.5

2.02E-02

-1.9

9.45E-05

COX7A1 GCDH

cytochrome c oxidase subunit VIIa polypeptide 1 (muscle) glutaryl-Coenzyme A dehydrogenase

-1.8 -1.3

4.53E-07 2.33E-01

-1.9 -2.0

1.66E-08 1.54E-03

ALDH4A1 UNG

aldehyde dehydrogenase 4 family, member A1 uracil-DNA glycosylase

-1.4 -1.8

5.53E-03 1.02E-02

-2.0 -2.1

1.71E-06 4.44E-04

FAM65B SLC25A34

family with sequence similarity 65, member B solute carrier family 25, member 34

-1.6 -1.6

3.66E-02 8.39E-03

-2.1 -2.1

9.01E-04 2.01E-05

BCKDHA

branched chain keto acid dehydrogenase E1, alpha polypeptide

-1.3

6.40E-02

-2.2

7.49E-07

PDP2 LDHD

pyruvate dehydrogenase phosphatase isoenzyme 2 lactate dehydrogenase D

-1.7 -1.6

1.43E-03 4.97E-03

-2.3 -2.3

1.45E-06 1.75E-06

UCP3

uncoupling protein 3 (mitochondrial, proton carrier)

-1.2

6.42E-01

-2.6

1.72E-03

69

Antioxidants & Redox Signaling Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila (doi: 10.1089/ars.2013.5432) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

70Page 70 of 70

ACSL6

acyl-CoA synthetase long-chain family member 6

-3.3

5.90E-03

-3.1

2.76E-03

GCAT OGDHL MAOB MFN2

glycine C-acetyltransferase (2-amino-3ketobutyrate coenzyme A ligase) oxoglutarate dehydrogenase-like monoamine oxidase B mitofusin 2

-2.0 -3.7 -5.3 -7.1

1.72E-03 2.32E-05 1.35E-06 6.99E-11

-3.2 -4.6 -4.7 -5.7

1.50E-06 5.22E-07 5.41E-07 4.02E-11

70

Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila.

Mitofusin (Mfn)2 redundantly promotes mitochondrial outer membrane tethering and organelle fusion with Mfn1, and uniquely functions as the mitochondri...
2MB Sizes 0 Downloads 0 Views