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Proteomics 2014, 14, 2105–2107
Editorial Proteomics in Chromatin Biology and Epigenetics Chromatin has a privileged role in the life of the cell. The feature most intimate with the genetic material, chromatin is the first layer of regulatory logic controlling gene expression and the final sensor for processes (internal and external) intent on changing cellular phenotype. Eukaryotic genomes have evolved to package themselves according to functional units of nucleosomes, octomeric protein complexes containing two copies of four core histones, which are in turn regulated extensively by protein interactions and post-translational modifications. How different nucleosomes control chromatin accessibility in different genomes (say, between species, or within a species between cell types), at what structural scales chromatin function is modulated and how accessibility changes over time (in development, disease and evolution), are some of the most pressing questions in all of biology. Epigenetic control of development—or the process by which a cell learns, and then subsequently “remembers”, to be another cell— has been long appreciated, with recent studies providing a new scale of detail about genome reprogramming and the nature of combinatorial specification of chromatin states. Moreover, it is now appreciated that chromatin modulation is a dynamic process in the physiology of health cells and that aberration in this process can be the cause and mechanism of various diseases. Our growing understanding of epigenetic mechanisms have been driven in large part by advancing technologies for high throughput, large scale ‘omics measurements. Excellent reviews exist on the recent growth of transcriptomics, genomics and epigenomics technology and applications. The objective of this Special Issue is to highlight the leading edge of proteomic methodology and concept as applied to epigenetics. One of the key mysteries of transcriptional regulation remains how RNA polymerase II (RNAPII) selects the right genes to transcribe at any moment in a given cell. One approach to understand this problem includes dissecting the protein complexes that regulate RNAPII localization, function, and/or elongation. Lijsebettens et al. (Elongator and SPT4/SPT5 complexes as proxy to study RNA polymerase II transcript elongation control in plant development. Viewpoint, pages 2109–2114) explore this area in their Viewpoint on Elongator function in RNAPII-mediated transcription. Distinct Elongator containing complexes were found to be associated with distinct gene expression targets in Arabidopsis development. Accordingly, these complexes were also shown to be associated with different phenotypes, including in the context of development and stress-response. This paper reveals the nuance of transcriptional regulation that can be appreciated only with unbiased techniques to dissect protein complexes involved in context-specific cellular functions, because in a different context the same protein may behave quite different. Karbassi and Vondriska (How the proteome packages the genome for cardiovascular development. Review, pages 2115–2126) review the state of the field of cardiovascular epigenomics with a particular emphasis on development. Recent studies have leveraged chromatin immunoprecipitation plus DNA sequencing, next generation RNA sequencing and proteomics to reveal the networks of molecules involved in specifying cardiovascular lineages. Some investigations have also begun to apply these techniques to disease, which can be associated with phenotypes reminiscent of development. The authors suggest that a frontier of chromatin regulation in development of the cardiovascular system and other organs is the understanding of the heterogeneity of protein complexes (and therein, local chromatin structure) at given loci and how this controls specific gene expression programs. Bigeard et al. (Phosphorylation-dependent regulation of plant chromatin and chromatinassociated proteins. Review, pages 2127–2140) review a distinct area of biology in which proteomics is having a major impact on our understanding of chromatin function. As with many modifications observable on proteins, the authors highlight the importance of understanding C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Thomas M. Vondriska
Ole N. Jensen
www.proteomics-journal.com
2106
Proteomics 2014, 14, 2105–2107
whether and how phosphorylation affects chromatin protein function. Mass spectrometry has driven the identification of phosphorylation sites in Arabidopsis (the focus of this review) and other species, revealing several chromatin-associated proteins to be targets of dynamic modification during plant development. These include chromatin structural proteins like histones but also other chromatin modifying enzymes, highlighting one manner in which signaling pathways, sometimes originating in other organelles, can directly impinge upon chromatin to affect gene expression. The next paper is by the same group, Bigeard et al. (Proteomic and phosphoproteomic analyses of chromatin-associated proteins in Arabidopsis thaliana. Research Article, pages 2141–2155), in which they report a novel dataset using a pipeline of immobilized metal anion affinity chromatography (IMAC) coupled with LC/MS/MS of enriched phospho-peptides using a high mass accuracy instrument. Nuclei were isolated and fractionated into low and high salt fractions, presumably reflecting the physical-chemical nature of the proteins’ association with DNA. These fractions hosted distinct proteins and distinct phosphorylation events, suggesting that this method of fractionation targets biologically meaningful subsets of the proteome. This workflow is likely to be very useful for others studying the model species Arabidopsis and should advance our ability to probe sub-nuclear functions, given that this method was effective in reproducibly identifying numerous sites of modification that have eluded previous proteomic investigations of the plant. Guise et al. also examined the role of phosphorylation to influence chromatin function with a specific focus on how the PTM affects protein interactions (Probing phosphorylationdependent protein interactions within functional domains of histone deacetylase 5. Research Article, pages 2156–2166). HDACs are an interesting class of molecule with a known role in modifying histones to influence gene expression. One of the key unknowns in this area is how HDAC isoforms distinguish between individual nucleosomes across the genome to elicit precise control of transcription. Focusing on HDAC5 due to its role in mitosis, the authors exhaustively characterize the sites of modification within this protein, linking them to protein structure. Next, mutant HDAC5 proteins are expressed in vivo and their localization, and more importantly, protein interactors are characterized by mass spectrometry. Different HDAC5 mutant were shown to form distinct protein interaction networks in the cell. In an additional layer of innovation, the investigators designed parallel reaction monitoring assays to quantify specific target peptides (and modifications) in different protein complexes associated with different versions of HDAC5. This study has fundamental implications for HDAC function and also presents a novel integrated method to studying PTM, protein interactions and signal transduction. Barth et al. examined the subproteome of molecules associated with the centromere, a key anatomical feature of genomes associated with cell division (Identification of novel Drosophila centromere-associated proteins. Research Article, pages 2167–2178). This study combined affinity isolation of a centromere-specific chromatin structural protein (CENP-ACID ), with micrococcal nuclease digestion to break down large chromatin fibers, followed by protein identification and label-free quantitation by Orbitrap mass spectrometry. Because a histone H3-tagged protein was used as a control, proteins specific to chromatin in the centromere could be identified with this approach. To investigate the candidate pool of proteins, the investigators turned to in vivo expression and immunohistochemistry, determining which of the proteins showed specific localization to Drosophila mitotic cells. Furthermore, knockdown of targeted proteins was carried out with functional readouts of localization and mitosis, revealing that several of the identified proteins were necessary for mitosis in these cells. Together these analyses are a great example of orthogonal techniques (affinity isolation, mass spectrometry and fluorescence confocal microscopy) to establish new mechanisms of chromatin structure in a specific sub-nuclear domain. The manner in which DNA methylation communicates with the protein component of chromatin for specification of accessibility and transcription is unknown. Baymaz et al. investigate this question from the standpoint of methyl-CpG-binding proteins (which can bind to methylated cytosines) and their interaction with the histone modifying polycomb repressive complex (MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpGbinding domain. Research Article, pages 2179–2189). SILAC-based quantitative proteomics, combined with affinity tag-based protein purification, determined that both the MBD5 and 6 isoforms bind the PR-DUB component of the polycomb complex, along with numerous other
C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
Proteomics 2014, 14, 2105–2107
2107
proteins. The interaction between MBD5 and PR-DUB was found to be dependent on the MBD domain of the former, revealing a novel role for this domain. Meanwhile MBD6 was shown to interact with a group of genes also occupied by the FoxK2 subunit of the PR-DUB complex and is recruited to sites of DNA damage in vivo. Together, these studies identify new hypotheses for how DNA methylation may be read by DNA binding proteins and how these proteins in turn can influence chromatin structural remodelers (in this case, transcriptional silencing machinery) and gene expression. The time scale over which PTMs are added to and removed from proteins is an emerging field, with particular importance for understanding how chromatin dynamics correspond to transient versus more enduring transcriptional and phenotypic change. Zheng et al. investigate the stability of histone modifications with a focus on histone H3 (Site specific human histone H3 methylation stability: fast K4me3 turnover. Research Article, pages 2190–2199), the core nucleosomal histone most well studied in terms of functional PTMs. A meticulous set of experiments combined pulse-chase metabolic labeling of HeLa cells, SILAC and SRM-based peptide quantitation and time course experiments to detect the portion of a total pool of H3 protein that was decorated with a given modification. Several interesting patterns revealed themselves. First, the longer a histone was around, the more methylated it became. Second, different residues were modified at varying rates, with H3K4me3 (an activating mark) having very rapid turnover. Third, different degrees of modification on the same residue exhibit distinct rates of stability (e.g. H3K4me3 turnover is fast, but H3K4me1 turnover is slow, whereas H3K9me1 turnover is fast, H3K9me3 slow). These studies add a critical new dimension to our understanding of chromatin regulation, exploring the stability of histone PTMs as a means of regulation. Recent studies, driven primarily by ChIP-DNA sequencing experiments and bioinformatics analysis, have emphasized the combinatorial role of histone PTMs to specify chromatin states and transcriptional events. However, these genomic approaches cannot resolve which modifications occur on the same histone molecule and/or the same nucleosome, a key feature for understanding the regulatory logic for how histone PTMs operate. Two papers in this issue report technical innovations to more thoroughly identify and quantify combinations of histone PTMs. Sidoli et al. describe a middle-down proteomics workflow in which high mass accuracy RP/HILIC/MS/MS of large peptides (from GluC digestion) is used to separate and identify coexisting PTMs—that is, modifications existing on the same physical molecule (Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones. Research Article, pages 2200–2211). ETDbased fragmentation in a middle-down analytical platform was critical to obtain good coverage of histone tails. This approach was facilitated by combining RP and HILIC separations with MS/MS and a novel suite of proteomic software that the authors have invented specifically for the analysis of histone proteins with multiple PTMs, called Histone Coder and isoScale, which are shown to reliably identify histone PTMs, quantify them and accurately assign residue(s) of modification. These informative tools are exhaustively tested in a series of experiments from cells in which a component of the polycomb repressive complex (Suz12) is disrupted. This MS-informatics approach allowed for an unprecendented accuracy and comprehensiveness in the quantitation of co-existing histone modifications in embryonic stem cells. Soldi et al. address the same challenge of co-existing PTMs on histones using a somewhat distinct mass spectrometry approach: ArgC digestion, nanoUPLC, and Orbitrap/QExactive mass spectrometry (Improved bottom-up strategy to efficiently separate hyper-modified histone peptides through ultra-HPLC separation on a benchtop Orbitrap instrument. Research Article, pages 2212–2225). Key innovations presented in this manuscript include the ability of the ultraHPLC to resolve more species of histone H3 and H4 than previously reported, including with excellent sequence coverage, facilitating reliable assignment of PTM status. This technology platform was then applied to characterize the temporal signature of histone PTMs on H3 and H4 in the setting of lipopolysaccharide stimulation, enabling the comprehensive quantitation of histone H3/H4 PTMs on a temporal basis. These two approaches for characterizing the totality of histone modifications can in principle be applied to all histone isoforms, to nonhistone chromatin proteins and in virtually any cell/tissue from which histones can be highly enriched. Finally, Britton et al. explored the modifications to host chromatin following infection with the human immunodeficiency virus (HIV) (A proteomic glimpse into the initial global
C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
2108
Proteomics 2014, 14, 2105–2107
epigenetic changes during HIV infection. Dataset Brief, pages 2226–2230). In a time course experiment, the authors infected SUP-T1 cells (human T cell line) with competent HIV or a version of the virus inactivated by ultraviolet light, the latter serving as a control of sorts to the host chromatin response to infection, rather than subsequent HIV integration into the host genome. LC/MS/MS of trypsin digested, propionic anhydride treated peptides using techniques established in this laboratory was then used to quantify modified histone molecules (and some other chromatin modifying enzymes) after infection. This initial study revealed that the principle chromatin response was due to infection, not integration of HIV into the host genome, paving the way for future studies into the transcriptional regulatory events associated with viral infection and replication. The reports in this Special Issue nicely demonstrate how various proteomics strategies contribute to elucidation of molecular features of proteins and protein networks involved in chromatin maintenance, transcriptional regulation and epigenetic mechanisms. We thank all the contributors for their efforts to present their research in this Special Issue.
Thomas M. Vondriska
C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Ole N. Jensen
www.proteomics-journal.com
Proteomics 2014, 14, 2105–2107
Editorial Proteomics in Chromatin Biology and Epigenetics Chromatin has a privileged role in the life of the cell. The feature most intimate with the genetic material, chromatin is the first layer of regulatory logic controlling gene expression and the final sensor for processes (internal and external) intent on changing cellular phenotype. Eukaryotic genomes have evolved to package themselves according to functional units of nucleosomes, octomeric protein complexes containing two copies of four core histones, which are in turn regulated extensively by protein interactions and post-translational modifications. How different nucleosomes control chromatin accessibility in different genomes (say, between species, or within a species between cell types), at what structural scales chromatin function is modulated and how accessibility changes over time (in development, disease and evolution), are some of the most pressing questions in all of biology. Epigenetic control of development—or the process by which a cell learns, and then subsequently “remembers”, to be another cell— has been long appreciated, with recent studies providing a new scale of detail about genome reprogramming and the nature of combinatorial specification of chromatin states. Moreover, it is now appreciated that chromatin modulation is a dynamic process in the physiology of health cells and that aberration in this process can be the cause and mechanism of various diseases. Our growing understanding of epigenetic mechanisms have been driven in large part by advancing technologies for high throughput, large scale ‘omics measurements. Excellent reviews exist on the recent growth of transcriptomics, genomics and epigenomics technology and applications. The objective of this Special Issue is to highlight the leading edge of proteomic methodology and concept as applied to epigenetics. One of the key mysteries of transcriptional regulation remains how RNA polymerase II (RNAPII) selects the right genes to transcribe at any moment in a given cell. One approach to understand this problem includes dissecting the protein complexes that regulate RNAPII localization, function, and/or elongation. Lijsebettens et al. (Elongator and SPT4/SPT5 complexes as proxy to study RNA polymerase II transcript elongation control in plant development. Viewpoint, pages 2109–2114) explore this area in their Viewpoint on Elongator function in RNAPII-mediated transcription. Distinct Elongator containing complexes were found to be associated with distinct gene expression targets in Arabidopsis development. Accordingly, these complexes were also shown to be associated with different phenotypes, including in the context of development and stress-response. This paper reveals the nuance of transcriptional regulation that can be appreciated only with unbiased techniques to dissect protein complexes involved in context-specific cellular functions, because in a different context the same protein may behave quite different. Karbassi and Vondriska (How the proteome packages the genome for cardiovascular development. Review, pages 2115–2126) review the state of the field of cardiovascular epigenomics with a particular emphasis on development. Recent studies have leveraged chromatin immunoprecipitation plus DNA sequencing, next generation RNA sequencing and proteomics to reveal the networks of molecules involved in specifying cardiovascular lineages. Some investigations have also begun to apply these techniques to disease, which can be associated with phenotypes reminiscent of development. The authors suggest that a frontier of chromatin regulation in development of the cardiovascular system and other organs is the understanding of the heterogeneity of protein complexes (and therein, local chromatin structure) at given loci and how this controls specific gene expression programs. Bigeard et al. (Phosphorylation-dependent regulation of plant chromatin and chromatinassociated proteins. Review, pages 2127–2140) review a distinct area of biology in which proteomics is having a major impact on our understanding of chromatin function. As with many modifications observable on proteins, the authors highlight the importance of understanding C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Thomas M. Vondriska
Ole N. Jensen
www.proteomics-journal.com
2106
Proteomics 2014, 14, 2105–2107
whether and how phosphorylation affects chromatin protein function. Mass spectrometry has driven the identification of phosphorylation sites in Arabidopsis (the focus of this review) and other species, revealing several chromatin-associated proteins to be targets of dynamic modification during plant development. These include chromatin structural proteins like histones but also other chromatin modifying enzymes, highlighting one manner in which signaling pathways, sometimes originating in other organelles, can directly impinge upon chromatin to affect gene expression. The next paper is by the same group, Bigeard et al. (Proteomic and phosphoproteomic analyses of chromatin-associated proteins in Arabidopsis thaliana. Research Article, pages 2141–2155), in which they report a novel dataset using a pipeline of immobilized metal anion affinity chromatography (IMAC) coupled with LC/MS/MS of enriched phospho-peptides using a high mass accuracy instrument. Nuclei were isolated and fractionated into low and high salt fractions, presumably reflecting the physical-chemical nature of the proteins’ association with DNA. These fractions hosted distinct proteins and distinct phosphorylation events, suggesting that this method of fractionation targets biologically meaningful subsets of the proteome. This workflow is likely to be very useful for others studying the model species Arabidopsis and should advance our ability to probe sub-nuclear functions, given that this method was effective in reproducibly identifying numerous sites of modification that have eluded previous proteomic investigations of the plant. Guise et al. also examined the role of phosphorylation to influence chromatin function with a specific focus on how the PTM affects protein interactions (Probing phosphorylationdependent protein interactions within functional domains of histone deacetylase 5. Research Article, pages 2156–2166). HDACs are an interesting class of molecule with a known role in modifying histones to influence gene expression. One of the key unknowns in this area is how HDAC isoforms distinguish between individual nucleosomes across the genome to elicit precise control of transcription. Focusing on HDAC5 due to its role in mitosis, the authors exhaustively characterize the sites of modification within this protein, linking them to protein structure. Next, mutant HDAC5 proteins are expressed in vivo and their localization, and more importantly, protein interactors are characterized by mass spectrometry. Different HDAC5 mutant were shown to form distinct protein interaction networks in the cell. In an additional layer of innovation, the investigators designed parallel reaction monitoring assays to quantify specific target peptides (and modifications) in different protein complexes associated with different versions of HDAC5. This study has fundamental implications for HDAC function and also presents a novel integrated method to studying PTM, protein interactions and signal transduction. Barth et al. examined the subproteome of molecules associated with the centromere, a key anatomical feature of genomes associated with cell division (Identification of novel Drosophila centromere-associated proteins. Research Article, pages 2167–2178). This study combined affinity isolation of a centromere-specific chromatin structural protein (CENP-ACID ), with micrococcal nuclease digestion to break down large chromatin fibers, followed by protein identification and label-free quantitation by Orbitrap mass spectrometry. Because a histone H3-tagged protein was used as a control, proteins specific to chromatin in the centromere could be identified with this approach. To investigate the candidate pool of proteins, the investigators turned to in vivo expression and immunohistochemistry, determining which of the proteins showed specific localization to Drosophila mitotic cells. Furthermore, knockdown of targeted proteins was carried out with functional readouts of localization and mitosis, revealing that several of the identified proteins were necessary for mitosis in these cells. Together these analyses are a great example of orthogonal techniques (affinity isolation, mass spectrometry and fluorescence confocal microscopy) to establish new mechanisms of chromatin structure in a specific sub-nuclear domain. The manner in which DNA methylation communicates with the protein component of chromatin for specification of accessibility and transcription is unknown. Baymaz et al. investigate this question from the standpoint of methyl-CpG-binding proteins (which can bind to methylated cytosines) and their interaction with the histone modifying polycomb repressive complex (MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpGbinding domain. Research Article, pages 2179–2189). SILAC-based quantitative proteomics, combined with affinity tag-based protein purification, determined that both the MBD5 and 6 isoforms bind the PR-DUB component of the polycomb complex, along with numerous other
C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
Proteomics 2014, 14, 2105–2107
2107
proteins. The interaction between MBD5 and PR-DUB was found to be dependent on the MBD domain of the former, revealing a novel role for this domain. Meanwhile MBD6 was shown to interact with a group of genes also occupied by the FoxK2 subunit of the PR-DUB complex and is recruited to sites of DNA damage in vivo. Together, these studies identify new hypotheses for how DNA methylation may be read by DNA binding proteins and how these proteins in turn can influence chromatin structural remodelers (in this case, transcriptional silencing machinery) and gene expression. The time scale over which PTMs are added to and removed from proteins is an emerging field, with particular importance for understanding how chromatin dynamics correspond to transient versus more enduring transcriptional and phenotypic change. Zheng et al. investigate the stability of histone modifications with a focus on histone H3 (Site specific human histone H3 methylation stability: fast K4me3 turnover. Research Article, pages 2190–2199), the core nucleosomal histone most well studied in terms of functional PTMs. A meticulous set of experiments combined pulse-chase metabolic labeling of HeLa cells, SILAC and SRM-based peptide quantitation and time course experiments to detect the portion of a total pool of H3 protein that was decorated with a given modification. Several interesting patterns revealed themselves. First, the longer a histone was around, the more methylated it became. Second, different residues were modified at varying rates, with H3K4me3 (an activating mark) having very rapid turnover. Third, different degrees of modification on the same residue exhibit distinct rates of stability (e.g. H3K4me3 turnover is fast, but H3K4me1 turnover is slow, whereas H3K9me1 turnover is fast, H3K9me3 slow). These studies add a critical new dimension to our understanding of chromatin regulation, exploring the stability of histone PTMs as a means of regulation. Recent studies, driven primarily by ChIP-DNA sequencing experiments and bioinformatics analysis, have emphasized the combinatorial role of histone PTMs to specify chromatin states and transcriptional events. However, these genomic approaches cannot resolve which modifications occur on the same histone molecule and/or the same nucleosome, a key feature for understanding the regulatory logic for how histone PTMs operate. Two papers in this issue report technical innovations to more thoroughly identify and quantify combinations of histone PTMs. Sidoli et al. describe a middle-down proteomics workflow in which high mass accuracy RP/HILIC/MS/MS of large peptides (from GluC digestion) is used to separate and identify coexisting PTMs—that is, modifications existing on the same physical molecule (Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones. Research Article, pages 2200–2211). ETDbased fragmentation in a middle-down analytical platform was critical to obtain good coverage of histone tails. This approach was facilitated by combining RP and HILIC separations with MS/MS and a novel suite of proteomic software that the authors have invented specifically for the analysis of histone proteins with multiple PTMs, called Histone Coder and isoScale, which are shown to reliably identify histone PTMs, quantify them and accurately assign residue(s) of modification. These informative tools are exhaustively tested in a series of experiments from cells in which a component of the polycomb repressive complex (Suz12) is disrupted. This MS-informatics approach allowed for an unprecendented accuracy and comprehensiveness in the quantitation of co-existing histone modifications in embryonic stem cells. Soldi et al. address the same challenge of co-existing PTMs on histones using a somewhat distinct mass spectrometry approach: ArgC digestion, nanoUPLC, and Orbitrap/QExactive mass spectrometry (Improved bottom-up strategy to efficiently separate hyper-modified histone peptides through ultra-HPLC separation on a benchtop Orbitrap instrument. Research Article, pages 2212–2225). Key innovations presented in this manuscript include the ability of the ultraHPLC to resolve more species of histone H3 and H4 than previously reported, including with excellent sequence coverage, facilitating reliable assignment of PTM status. This technology platform was then applied to characterize the temporal signature of histone PTMs on H3 and H4 in the setting of lipopolysaccharide stimulation, enabling the comprehensive quantitation of histone H3/H4 PTMs on a temporal basis. These two approaches for characterizing the totality of histone modifications can in principle be applied to all histone isoforms, to nonhistone chromatin proteins and in virtually any cell/tissue from which histones can be highly enriched. Finally, Britton et al. explored the modifications to host chromatin following infection with the human immunodeficiency virus (HIV) (A proteomic glimpse into the initial global
C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.proteomics-journal.com
2108
Proteomics 2014, 14, 2105–2107
epigenetic changes during HIV infection. Dataset Brief, pages 2226–2230). In a time course experiment, the authors infected SUP-T1 cells (human T cell line) with competent HIV or a version of the virus inactivated by ultraviolet light, the latter serving as a control of sorts to the host chromatin response to infection, rather than subsequent HIV integration into the host genome. LC/MS/MS of trypsin digested, propionic anhydride treated peptides using techniques established in this laboratory was then used to quantify modified histone molecules (and some other chromatin modifying enzymes) after infection. This initial study revealed that the principle chromatin response was due to infection, not integration of HIV into the host genome, paving the way for future studies into the transcriptional regulatory events associated with viral infection and replication. The reports in this Special Issue nicely demonstrate how various proteomics strategies contribute to elucidation of molecular features of proteins and protein networks involved in chromatin maintenance, transcriptional regulation and epigenetic mechanisms. We thank all the contributors for their efforts to present their research in this Special Issue.
Thomas M. Vondriska
C 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Ole N. Jensen
www.proteomics-journal.com
