TRANSCRIPTION 2016, VOL. 7, NO. 3, 91–95 http://dx.doi.org/10.1080/21541264.2016.1182240
POINT-OF-VIEW
Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription N. S. Gerasimovaa, N. A. Pestovb, O. I. Kulaevaa,c, D. J. Clarkd, and V. M. Studitskya,b,c a Biology Faculty, Lomonosov Moscow State University, Moscow, Russia; bDepartment of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA; cCancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, USA; dDivision of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
ABSTRACT
ARTICLE HISTORY
RNA polymerase II (Pol II) transcription through chromatin is accompanied by formation of small intranucleosomal DNA loops. Pol II captured within a small loop drives accumulation of DNA supercoiling, facilitating further transcription. DNA breaks relieve supercoiling and induce Pol II arrest, allowing detection of DNA damage hidden in chromatin structure.
Received 6 April 2016 Accepted 19 April 2016
Topologically locked DNA can be under-wound (negatively supercoiled) or over-wound (positively supercoiled). DNA supercoiling is partitioned between changes in the number of base pairs per turn of the double helix (the DNA twist, Fig. 1A) and in its threedimensional geometry (writhe, Fig. 1B). Many events occurring on DNA alter its topological state. Both DNA and RNA polymerases are powerful molecular motors. In particular, transcription of the double helix requires rotation of the elongation complex relative to DNA. If rotation of the enzyme is impeded (e.g. due to association of the enzyme with a subcellular structure, or by viscous drag on the RNA and associated proteins as they try to rotate with the RNA polymerase), its progression along the righthanded DNA double helix generates twin domains of positive and negative DNA supercoiling ahead and behind the enzyme, respectively1 (Figs. 1A and B). Eukaryotic genomic DNA is not protein-free but packed into chromatin. In the nucleosome—the fundamental unit of chromatin2—DNA is wrapped around a central core histone octamer, protecting about one negative supercoil from relaxation by topoisomerases.3 The majority of genomic DNA
KEYWORDS
chromatin; DNA repair; DNA supercoiling; elongation; intermediates; intranucleosomal DNA loops; mechanism; nucleosome; RNA polymerase II; single strand DNA breaks; structure; transcription
within nuclei is relaxed due to the action of topoisomerases.4 Nevertheless, negatively supercoiled domains can also be found in the presence of active topoisomerases.5 Topological domains in eukaryotic cells can be formed by nucleosome boundaries, polymerases and specific domain-associated proteins.6 The twin-supercoiled-domain model is applicable to eukaryotic transcription.7 It could provide realtime feedback during transcript elongation, because it may affect chromatin decondensation in the gene body and modulate chromatin structure in nearby regions (reviewed in ref.5,6). Our recent studies in vitro have revealed that small intra-nucleosomal DNA loops (i-loops) are formed transiently during transcription through a nucleosome.8–10 These loops play a major role in the progression of RNA polymerase through nucleosomes. Furthermore, they may facilitate detection of DNA damage hidden within nucleosomes.9 During elongation, RNA polymerase II (Pol II) encounters a nucleosome every »200 bp (the average nucleosome spacing in higher eukaryotes). Transcription of genes by Pol II at a moderate level is accompanied by retention of core histones on the DNA, although at higher levels of
CONTACT V. M. Studitsky [email protected] Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA. Color versions of one or more of the figures in this article can be found online at www.tandfonline.com/ktrn. © 2016 Taylor & Francis Group, LLC
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Figure 1. Transcription-driven DNA supercoiling and intra-nucleosomal DNA loops (i-loops). (A, B) The twin-supercoiled domain model.1 (A) Progression of RNA polymerase within a topologically locked DNA domain can result in generation of positive and negative DNA supercoils ahead and behind of the enzyme. (B) DNA-binding proteins (like CTCF protein24) can form topological barriers in living cells enabling accumulation of unconstrained transcription-driven supercoiling. (C) Pol II transcription through a nucleosome leads to formation of i-loops having slightly different sizes and containing the transcribing enzyme.8,9 On the right: When the active center of Pol II reaches 24, 34 or 44 bp into the nucleosome, small i-loops with about 15–20 bp on either side of the polymerase are formed when the active center of Pol II is at the position 24, 34 or 44 bp in a nucleosome.9 On the left: When the polymerase is at the position 49 bp from the boundary, an even smaller i-loop ( ; -loop) is formed. The small loops form topologically locked domains preventing rotation of the enzyme: as Pol II attempts to rotate, positive and negative DNA supercoils accumulate ahead and behind of the enzyme, respectively. The loops must be opened either in front or behind Pol II to allow its further progression.
transcription they can be lost, with preferential loss of H2A/H2B histones.11 Nucleosome survival during transcription by Pol II occurs through formation of iloops containing the transcribing enzyme. In the case of RNA polymerase III (Pol III), the formation of larger i-loops likely facilitates nucleosome translocation from in front to behind the enzyme.12 However, Pol II is different: two types of i-loop are formed by Pol II, depending on its location within the nucleosome. When the active center of Pol II reaches 24, 34 or 44 bp into the nucleosome, small i-loops with about 15–20 bp on either side of the polymerase are formed (Fig. 1C).9 When the polymerase reaches farther into the nucleosome, at 49 bp from the boundary, an even smaller i-loop is formed (Fig. 1C).8 I-loops forming during transcription represent topologically locked domains with an enclosed molecular motor. Progression of Pol II within an i-loop likely leads to accumulation of supercoiling in the looped DNA ahead of and behind the enzyme (Fig. 1C). Due to the small size of the
loop, supercoiling would primarily affect DNA twist. These changes in twist could have important consequences for transcription. To relieve the supercoiling stress, DNA–histone interactions in front and/or behind the RNA polymerase could be disrupted, inducing opening of the loop and strongly facilitating further transcription (Figs. 2A and B). The opening occurs on one side of the loop and relieves accumulated DNA supercoiling.9 The i-loops formed 24, 34 and 44 bp within the nucleosome are opened behind the enzyme, whereas the i-loop formed at 49 bp is opened ahead of Pol II.8,9 It should be noted that a nucleosome with an i-loop formed at 49 bp contains more DNA–histone interactions in front of the enzyme than behind it, yet the i-loop is disrupted in front of Pol II.8 Thus, DNA–histone interactions are more efficiently destabilized by positive DNA supercoiling accumulated ahead of Pol II (discussed in ref.13). This finding is consistent with the fact that nucleosomes formed on positively supercoiled DNA are less stable than nucleosomes
TRANSCRIPTION
93
Figure 2. Roles of i-loops. Several important functions for i-loops have been suggested.9 Both negative and positive supercoiling could disrupt DNA–histone interactions and open the loop, thus facilitating further transcription through the nucleosome (pathway 1) accompanied by nucleosome survival or backward translocation (pathway 2). Note that both positive (pathway 1) and negative DNA supercoiling (pathway 2) can accumulate even after the i-loop is opened behind the polymerase (pathway 1) or in front of the polymerase (pathway 2), if rotation of the enzyme is still inhibited by DNA–histone interactions (topological locks) in front of or behind the enzyme, respectively. DNA supercoiling accumulated after i-loop formation can serve as a sensor for single-stranded DNA breaks (pathway 3). When the break (indicated by the star) is located behind the enzyme, it can cause arrest of transcribing Pol II in the i-loop.
formed on negatively supercoiled DNA in vitro14 and with the idea that positive supercoiling inhibits nucleosome assembly and occupancy.15 These data suggest that nucleosomes are more vulnerable to positive twist than to positive writhe.14,15 Both negative and positive DNA supercoiling can accumulate in front of and behind the enzyme, respectively, without the formation of an i-loop, if rotation of the enzyme is sterically inhibited by DNA–histone interactions (topological locks) (Fig. 2, pathways 1 and 2). This effect likely operates both before and after i-loop formation.9 Positive DNA supercoiling accumulated in front of RNA polymerase might also induce unfolding of the histone octamer together with nucleosomal DNA.16 I-loops and intra-nucleosomal DNA supercoiling likely play a role in recognition of DNA damage hidden in chromatin structure (Fig. 2, pathway 3). A single strand break (SSB) within an i-loop could act like a swivel, relieving previously accumulated DNA supercoiling. SSBs located in front of or behind a
transcribing polymerase likely facilitate or inhibit progression of the enzyme through nucleosome-specific pauses, respectively.9 In particular, an SSB present in the non-template DNA strand could relieve DNA supercoiling accumulated in an i-loop and induce strong arrest of Pol II within the nucleosome. Thus, DNA supercoiling accumulated after i-loop formation can serve as a sensor of DNA damage. Pol II arrest is a signal for the transcription-coupled repair cascade; therefore, the ability of a nontemplate SSB to induce transcriptional arrest suggests a possible role in DNA repair. In higher eukaryotes, SSBs are detected by poly(ADP-ribose) polymerase (PARP1),17–19 but chromatin-organized DNA is likely less accessible to PARP1, and at least some lesions could remain undetected. SSBs located in the template strand of genes can be detected by Pol II arrest during transcription and repaired by the transcription-coupled nucleotide excision repair (TC-NER) pathway.20,21 Furthermore, repair of non-template SSBs requires the activity of CSB, the major TC-NER
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factor in mammalian cells,22 suggesting that the TCNER pathway is also involved in repair of non-template SSBs. Overall, transcription-dependent supercoiling facilitates nucleosome transcription.9 I-loops with enclosed Pol II are efficiently formed at different locations within the nucleosome. It suggests that the tendency to maintain the compact state during transcription (and perhaps during other DNA transactions) is a fundamental property of nucleosomes. Formation of compact complexes with a large number of DNA–histone contacts likely decreases the probability of loss of the histone octamer during transcription and thus results in more efficient nucleosome survival. Formation of i-loops is especially important before position C49, where the loop forms for the last time and resolves in front of the transcribing complex, resulting in nucleosome recovery and further efficient transcription along DNA uncoiled from the surface of the histone octamer.8 In vivo and in vitro studies have revealed that chromatin remodeling is also accompanied by formation of DNA loops.23 Thus, i-loops could facilitate nucleosome survival and/or progression of other processive enzymes (e.g., eukaryotic replisome) along DNA.
Disclosure of potential conflicts of interest No potential conflicts of interest were disclosed.
Funding This work was supported by NIH grant GM58650 to V.M.S. by the Russian Science Foundation (RSF grant No. 14-24-00031), and by Intramural Research Program of the National Institutes of Health (NICHD) to D.J.C.
References [1] Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A 1987; 84:7024–7027. [2] Luger K, M€ader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997; 389:251–260. [3] Teves SS, Henikoff S. DNA torsion as a feedback mediator of transcription and chromatin dynamics. Nucl Austin Tex 2014; 5:211–218. [4] Sinden RR, Carlson JO, Pettijohn DE. Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells. Cell 1980; 21:773–783.
[5] Hirose S, Matsumoto K. Possible Roles of DNA Supercoiling in Transcription. 2013 [cited 2016 Mar 25]; Available from: http://www.ncbi.nlm.nih.gov/ books/NBK6243/ [6] Kouzine F, Levens D, Baranello L. DNA topology and transcription. Nucl Austin Tex 2014; 5:195–202. [7] Giaever GN, Wang JC. Supercoiling of intracellular DNA can occur in eukaryotic cells. Cell 1988; 55:849–856. [8] Kulaeva OI, Gaykalova DA, Pestov NA, Golovastov VV, Vassylyev DG, Artsimovitch I, Studitsky VM. Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II. Nat Struct Mol Biol 2009; 16:1272–1278. [9] Pestov NA, Gerasimova NS, Kulaeva OI, Studitsky VM. Structure of transcribed chromatin is a sensor of DNA damage. Sci Adv 2015; 1:e1500021. [10] Gaykalova DA, Kulaeva OI, Volokh O, Shaytan AK, Hsieh FK, Kirpichnikov MP, Sokolova OS, Studitsky VM. Structural analysis of nucleosomal barrier to transcription. Proc Natl Acad Sci U S A 2015; 112:E5787– 5795. [11] Cole HA, Ocampo J, Iben JR, Chereji RV, Clark DJ. Heavy transcription of yeast genes correlates with differential loss of histone H2B relative to H4 and queued RNA polymerases. Nucleic Acids Res 2014; 42:12512– 12522. [12] Studitsky VM, Kassavetis GA, Geiduschek EP, Felsenfeld G. Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase. Science 1997; 278:1960–1963. [13] Studitsky VM, Clark DJ, Felsenfeld G. A histone octamer can step around a transcribing polymerase without leaving the template. Cell 1994; 76:371–382. [14] Clark DJ, Felsenfeld G. Formation of nucleosomes on positively supercoiled DNA. EMBO J 1991; 10:387–395. [15] Gupta P, Zlatanova J, Tomschik M. Nucleosome assembly depends on the torsion in the DNA molecule: a magnetic tweezers study. Biophys J 2009; 97:3150–3157. [16] Bancaud A, Wagner G, Conde E, Silva N, Lavelle C, Wong H, Mozziconacci J, Barbi M, Sivolob A, Le Cam E et al. Nucleosome chiral transition under positive torsional stress in single chromatin fibers. Mol Cell 2007; 27:135–147. [17] Caldecott KW. Single-strand break repair and genetic disease. Nat Rev Genet 2008; 9:619–631. [18] Weinfeld M, Chaudhry MA, D’Amours D, Pelletier JD, Poirier GG, Povirk LF, Lees-Miller SP. Interaction of DNA-dependent protein kinase and poly(ADP-ribose) polymerase with radiation-induced DNA strand breaks. Radiat Res 1997; 148:22–28. [19] Eustermann S, Wu WF, Langelier MF, Yang J-C, Easton LE, Riccio AA, Pascal JM, Neuhaus D. Structural Basis of Detection and Signaling of DNA SingleStrand Breaks by Human PARP-1. Mol Cell 2015; 60:742–754.
TRANSCRIPTION
[20] Wellinger RE, Thoma F. Nucleosome structure and positioning modulate nucleotide excision repair in the nontranscribed strand of an active gene. EMBO J 1997; 16:5046–5056. [21] Tijsterman M, de Pril R, Tasseron-de Jong JG, Brouwer J. RNA polymerase II transcription suppresses nucleosomal modulation of UV-induced (6-4) photoproduct and cyclobutane pyrimidine dimer repair in yeast. Mol Cell Biol 1999; 19:934–940. [22] Khobta A, Lingg T, Schulz I, Warken D, Kitsera N, Epe B. Mouse CSB protein is important for gene expression
95
in the presence of a single-strand break in the nontranscribed DNA strand. DNA Repair 2010; 9:985–993. [23] Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, Cairns BR, Peterson CL, Bustamante C. DNA Translocation and Loop Formation Mechanism of Chromatin Remodeling by SWI/SNF and RSC. Mol Cell 2006; 24:559–568. [24] Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012; 485:376–380.
POINT-OF-VIEW
Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription N. S. Gerasimovaa, N. A. Pestovb, O. I. Kulaevaa,c, D. J. Clarkd, and V. M. Studitskya,b,c a Biology Faculty, Lomonosov Moscow State University, Moscow, Russia; bDepartment of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA; cCancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA, USA; dDivision of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
ABSTRACT
ARTICLE HISTORY
RNA polymerase II (Pol II) transcription through chromatin is accompanied by formation of small intranucleosomal DNA loops. Pol II captured within a small loop drives accumulation of DNA supercoiling, facilitating further transcription. DNA breaks relieve supercoiling and induce Pol II arrest, allowing detection of DNA damage hidden in chromatin structure.
Received 6 April 2016 Accepted 19 April 2016
Topologically locked DNA can be under-wound (negatively supercoiled) or over-wound (positively supercoiled). DNA supercoiling is partitioned between changes in the number of base pairs per turn of the double helix (the DNA twist, Fig. 1A) and in its threedimensional geometry (writhe, Fig. 1B). Many events occurring on DNA alter its topological state. Both DNA and RNA polymerases are powerful molecular motors. In particular, transcription of the double helix requires rotation of the elongation complex relative to DNA. If rotation of the enzyme is impeded (e.g. due to association of the enzyme with a subcellular structure, or by viscous drag on the RNA and associated proteins as they try to rotate with the RNA polymerase), its progression along the righthanded DNA double helix generates twin domains of positive and negative DNA supercoiling ahead and behind the enzyme, respectively1 (Figs. 1A and B). Eukaryotic genomic DNA is not protein-free but packed into chromatin. In the nucleosome—the fundamental unit of chromatin2—DNA is wrapped around a central core histone octamer, protecting about one negative supercoil from relaxation by topoisomerases.3 The majority of genomic DNA
KEYWORDS
chromatin; DNA repair; DNA supercoiling; elongation; intermediates; intranucleosomal DNA loops; mechanism; nucleosome; RNA polymerase II; single strand DNA breaks; structure; transcription
within nuclei is relaxed due to the action of topoisomerases.4 Nevertheless, negatively supercoiled domains can also be found in the presence of active topoisomerases.5 Topological domains in eukaryotic cells can be formed by nucleosome boundaries, polymerases and specific domain-associated proteins.6 The twin-supercoiled-domain model is applicable to eukaryotic transcription.7 It could provide realtime feedback during transcript elongation, because it may affect chromatin decondensation in the gene body and modulate chromatin structure in nearby regions (reviewed in ref.5,6). Our recent studies in vitro have revealed that small intra-nucleosomal DNA loops (i-loops) are formed transiently during transcription through a nucleosome.8–10 These loops play a major role in the progression of RNA polymerase through nucleosomes. Furthermore, they may facilitate detection of DNA damage hidden within nucleosomes.9 During elongation, RNA polymerase II (Pol II) encounters a nucleosome every »200 bp (the average nucleosome spacing in higher eukaryotes). Transcription of genes by Pol II at a moderate level is accompanied by retention of core histones on the DNA, although at higher levels of
CONTACT V. M. Studitsky [email protected] Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA. Color versions of one or more of the figures in this article can be found online at www.tandfonline.com/ktrn. © 2016 Taylor & Francis Group, LLC
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N. S. GERASIMOVA ET AL.
Figure 1. Transcription-driven DNA supercoiling and intra-nucleosomal DNA loops (i-loops). (A, B) The twin-supercoiled domain model.1 (A) Progression of RNA polymerase within a topologically locked DNA domain can result in generation of positive and negative DNA supercoils ahead and behind of the enzyme. (B) DNA-binding proteins (like CTCF protein24) can form topological barriers in living cells enabling accumulation of unconstrained transcription-driven supercoiling. (C) Pol II transcription through a nucleosome leads to formation of i-loops having slightly different sizes and containing the transcribing enzyme.8,9 On the right: When the active center of Pol II reaches 24, 34 or 44 bp into the nucleosome, small i-loops with about 15–20 bp on either side of the polymerase are formed when the active center of Pol II is at the position 24, 34 or 44 bp in a nucleosome.9 On the left: When the polymerase is at the position 49 bp from the boundary, an even smaller i-loop ( ; -loop) is formed. The small loops form topologically locked domains preventing rotation of the enzyme: as Pol II attempts to rotate, positive and negative DNA supercoils accumulate ahead and behind of the enzyme, respectively. The loops must be opened either in front or behind Pol II to allow its further progression.
transcription they can be lost, with preferential loss of H2A/H2B histones.11 Nucleosome survival during transcription by Pol II occurs through formation of iloops containing the transcribing enzyme. In the case of RNA polymerase III (Pol III), the formation of larger i-loops likely facilitates nucleosome translocation from in front to behind the enzyme.12 However, Pol II is different: two types of i-loop are formed by Pol II, depending on its location within the nucleosome. When the active center of Pol II reaches 24, 34 or 44 bp into the nucleosome, small i-loops with about 15–20 bp on either side of the polymerase are formed (Fig. 1C).9 When the polymerase reaches farther into the nucleosome, at 49 bp from the boundary, an even smaller i-loop is formed (Fig. 1C).8 I-loops forming during transcription represent topologically locked domains with an enclosed molecular motor. Progression of Pol II within an i-loop likely leads to accumulation of supercoiling in the looped DNA ahead of and behind the enzyme (Fig. 1C). Due to the small size of the
loop, supercoiling would primarily affect DNA twist. These changes in twist could have important consequences for transcription. To relieve the supercoiling stress, DNA–histone interactions in front and/or behind the RNA polymerase could be disrupted, inducing opening of the loop and strongly facilitating further transcription (Figs. 2A and B). The opening occurs on one side of the loop and relieves accumulated DNA supercoiling.9 The i-loops formed 24, 34 and 44 bp within the nucleosome are opened behind the enzyme, whereas the i-loop formed at 49 bp is opened ahead of Pol II.8,9 It should be noted that a nucleosome with an i-loop formed at 49 bp contains more DNA–histone interactions in front of the enzyme than behind it, yet the i-loop is disrupted in front of Pol II.8 Thus, DNA–histone interactions are more efficiently destabilized by positive DNA supercoiling accumulated ahead of Pol II (discussed in ref.13). This finding is consistent with the fact that nucleosomes formed on positively supercoiled DNA are less stable than nucleosomes
TRANSCRIPTION
93
Figure 2. Roles of i-loops. Several important functions for i-loops have been suggested.9 Both negative and positive supercoiling could disrupt DNA–histone interactions and open the loop, thus facilitating further transcription through the nucleosome (pathway 1) accompanied by nucleosome survival or backward translocation (pathway 2). Note that both positive (pathway 1) and negative DNA supercoiling (pathway 2) can accumulate even after the i-loop is opened behind the polymerase (pathway 1) or in front of the polymerase (pathway 2), if rotation of the enzyme is still inhibited by DNA–histone interactions (topological locks) in front of or behind the enzyme, respectively. DNA supercoiling accumulated after i-loop formation can serve as a sensor for single-stranded DNA breaks (pathway 3). When the break (indicated by the star) is located behind the enzyme, it can cause arrest of transcribing Pol II in the i-loop.
formed on negatively supercoiled DNA in vitro14 and with the idea that positive supercoiling inhibits nucleosome assembly and occupancy.15 These data suggest that nucleosomes are more vulnerable to positive twist than to positive writhe.14,15 Both negative and positive DNA supercoiling can accumulate in front of and behind the enzyme, respectively, without the formation of an i-loop, if rotation of the enzyme is sterically inhibited by DNA–histone interactions (topological locks) (Fig. 2, pathways 1 and 2). This effect likely operates both before and after i-loop formation.9 Positive DNA supercoiling accumulated in front of RNA polymerase might also induce unfolding of the histone octamer together with nucleosomal DNA.16 I-loops and intra-nucleosomal DNA supercoiling likely play a role in recognition of DNA damage hidden in chromatin structure (Fig. 2, pathway 3). A single strand break (SSB) within an i-loop could act like a swivel, relieving previously accumulated DNA supercoiling. SSBs located in front of or behind a
transcribing polymerase likely facilitate or inhibit progression of the enzyme through nucleosome-specific pauses, respectively.9 In particular, an SSB present in the non-template DNA strand could relieve DNA supercoiling accumulated in an i-loop and induce strong arrest of Pol II within the nucleosome. Thus, DNA supercoiling accumulated after i-loop formation can serve as a sensor of DNA damage. Pol II arrest is a signal for the transcription-coupled repair cascade; therefore, the ability of a nontemplate SSB to induce transcriptional arrest suggests a possible role in DNA repair. In higher eukaryotes, SSBs are detected by poly(ADP-ribose) polymerase (PARP1),17–19 but chromatin-organized DNA is likely less accessible to PARP1, and at least some lesions could remain undetected. SSBs located in the template strand of genes can be detected by Pol II arrest during transcription and repaired by the transcription-coupled nucleotide excision repair (TC-NER) pathway.20,21 Furthermore, repair of non-template SSBs requires the activity of CSB, the major TC-NER
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factor in mammalian cells,22 suggesting that the TCNER pathway is also involved in repair of non-template SSBs. Overall, transcription-dependent supercoiling facilitates nucleosome transcription.9 I-loops with enclosed Pol II are efficiently formed at different locations within the nucleosome. It suggests that the tendency to maintain the compact state during transcription (and perhaps during other DNA transactions) is a fundamental property of nucleosomes. Formation of compact complexes with a large number of DNA–histone contacts likely decreases the probability of loss of the histone octamer during transcription and thus results in more efficient nucleosome survival. Formation of i-loops is especially important before position C49, where the loop forms for the last time and resolves in front of the transcribing complex, resulting in nucleosome recovery and further efficient transcription along DNA uncoiled from the surface of the histone octamer.8 In vivo and in vitro studies have revealed that chromatin remodeling is also accompanied by formation of DNA loops.23 Thus, i-loops could facilitate nucleosome survival and/or progression of other processive enzymes (e.g., eukaryotic replisome) along DNA.
Disclosure of potential conflicts of interest No potential conflicts of interest were disclosed.
Funding This work was supported by NIH grant GM58650 to V.M.S. by the Russian Science Foundation (RSF grant No. 14-24-00031), and by Intramural Research Program of the National Institutes of Health (NICHD) to D.J.C.
References [1] Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A 1987; 84:7024–7027. [2] Luger K, M€ader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997; 389:251–260. [3] Teves SS, Henikoff S. DNA torsion as a feedback mediator of transcription and chromatin dynamics. Nucl Austin Tex 2014; 5:211–218. [4] Sinden RR, Carlson JO, Pettijohn DE. Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells. Cell 1980; 21:773–783.
[5] Hirose S, Matsumoto K. Possible Roles of DNA Supercoiling in Transcription. 2013 [cited 2016 Mar 25]; Available from: http://www.ncbi.nlm.nih.gov/ books/NBK6243/ [6] Kouzine F, Levens D, Baranello L. DNA topology and transcription. Nucl Austin Tex 2014; 5:195–202. [7] Giaever GN, Wang JC. Supercoiling of intracellular DNA can occur in eukaryotic cells. Cell 1988; 55:849–856. [8] Kulaeva OI, Gaykalova DA, Pestov NA, Golovastov VV, Vassylyev DG, Artsimovitch I, Studitsky VM. Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II. Nat Struct Mol Biol 2009; 16:1272–1278. [9] Pestov NA, Gerasimova NS, Kulaeva OI, Studitsky VM. Structure of transcribed chromatin is a sensor of DNA damage. Sci Adv 2015; 1:e1500021. [10] Gaykalova DA, Kulaeva OI, Volokh O, Shaytan AK, Hsieh FK, Kirpichnikov MP, Sokolova OS, Studitsky VM. Structural analysis of nucleosomal barrier to transcription. Proc Natl Acad Sci U S A 2015; 112:E5787– 5795. [11] Cole HA, Ocampo J, Iben JR, Chereji RV, Clark DJ. Heavy transcription of yeast genes correlates with differential loss of histone H2B relative to H4 and queued RNA polymerases. Nucleic Acids Res 2014; 42:12512– 12522. [12] Studitsky VM, Kassavetis GA, Geiduschek EP, Felsenfeld G. Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase. Science 1997; 278:1960–1963. [13] Studitsky VM, Clark DJ, Felsenfeld G. A histone octamer can step around a transcribing polymerase without leaving the template. Cell 1994; 76:371–382. [14] Clark DJ, Felsenfeld G. Formation of nucleosomes on positively supercoiled DNA. EMBO J 1991; 10:387–395. [15] Gupta P, Zlatanova J, Tomschik M. Nucleosome assembly depends on the torsion in the DNA molecule: a magnetic tweezers study. Biophys J 2009; 97:3150–3157. [16] Bancaud A, Wagner G, Conde E, Silva N, Lavelle C, Wong H, Mozziconacci J, Barbi M, Sivolob A, Le Cam E et al. Nucleosome chiral transition under positive torsional stress in single chromatin fibers. Mol Cell 2007; 27:135–147. [17] Caldecott KW. Single-strand break repair and genetic disease. Nat Rev Genet 2008; 9:619–631. [18] Weinfeld M, Chaudhry MA, D’Amours D, Pelletier JD, Poirier GG, Povirk LF, Lees-Miller SP. Interaction of DNA-dependent protein kinase and poly(ADP-ribose) polymerase with radiation-induced DNA strand breaks. Radiat Res 1997; 148:22–28. [19] Eustermann S, Wu WF, Langelier MF, Yang J-C, Easton LE, Riccio AA, Pascal JM, Neuhaus D. Structural Basis of Detection and Signaling of DNA SingleStrand Breaks by Human PARP-1. Mol Cell 2015; 60:742–754.
TRANSCRIPTION
[20] Wellinger RE, Thoma F. Nucleosome structure and positioning modulate nucleotide excision repair in the nontranscribed strand of an active gene. EMBO J 1997; 16:5046–5056. [21] Tijsterman M, de Pril R, Tasseron-de Jong JG, Brouwer J. RNA polymerase II transcription suppresses nucleosomal modulation of UV-induced (6-4) photoproduct and cyclobutane pyrimidine dimer repair in yeast. Mol Cell Biol 1999; 19:934–940. [22] Khobta A, Lingg T, Schulz I, Warken D, Kitsera N, Epe B. Mouse CSB protein is important for gene expression
95
in the presence of a single-strand break in the nontranscribed DNA strand. DNA Repair 2010; 9:985–993. [23] Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, Cairns BR, Peterson CL, Bustamante C. DNA Translocation and Loop Formation Mechanism of Chromatin Remodeling by SWI/SNF and RSC. Mol Cell 2006; 24:559–568. [24] Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012; 485:376–380.
