http://www.epigeneticsandchromatin.com The latest research articles published by Epigenetics & Chromatin 2012-01-30T00:00:00Z The integrity of DNA is continuously challenged by metabolism-derived and environmental genotoxic agents that cause a variety of DNA lesions, including base alterations and breaks. DNA damage interferes with vital processes such as transcription and replication, and if not repaired properly, can ultimately lead to premature aging and cancer. Multiple DNA pathways signaling for DNA repair and DNA damage collectively safeguard the integrity of DNA. Chromatin plays a pivotal role in regulating DNA-associated processes, and is itself subject to regulation by the DNA-damage response. Chromatin influences access to DNA, and often serves as a docking or signaling site for repair and signaling proteins. Its structure can be adapted by post-translational histone modifications and nucleosome remodeling, catalyzed by the activity of ATP-dependent chromatin-remodeling complexes. In recent years, accumulating evidence has suggested that ATP-dependent chromatin-remodeling complexes play important, although poorly characterized, roles in facilitating the effectiveness of the DNA-damage response. In this review, we summarize the current knowledge on the involvement of ATP-dependent chromatin remodeling in three major DNA repair pathways: nucleotide excision repair, homologous recombination, and non-homologous end-joining. This shows that a surprisingly large number of different remodeling complexes display pleiotropic functions during different stages of the DNA-damage response. Moreover, several complexes seem to have multiple functions, and are implicated in various mechanistically distinct repair pathways. http://www.epigeneticsandchromatin.com/content/5/1/4 Hannes Lans Jurgen Marteijn Wim Vermeulen Epigenetics & Chromatin 2012, null:4 2012-01-30T00:00:00Z doi:10.1186/1756-8935-5-4 /content/figures/1756-8935-5-4-toc.gif Epigenetics & Chromatin 1756-8935 ${item.volume} 4 2012-01-30T00:00:00Z XML Background: DNA methylation, histone modifications and nucleosome occupancy act in concert for regulation of gene expression patterns in mammalian cells. Recently, G9a, a H3K9 methyltransferase, has been shown to play a role in establishment of DNA methylation at embryonic gene targets in ES cells through recruitment of de novo DNMT3A/3B enzymes. However, whether G9a plays a similar role in maintenance of DNA methylation in somatic cells is still unclear. Results: Here we show that G9a is not essential for maintenance of DNA methylation in somatic cells. Knockdown of G9a has no measurable effect on DNA methylation levels at G9a-target loci. DNMT3A/3B remain stably anchored to nucleosomes containing methylated DNA even in the absence of G9a, ensuring faithful propagation of methylated states in cooperation with DNMT1 through somatic divisions. Moreover, G9a also associates with nucleosomes in a DNMT3A/3B and DNA methylation-independent manner. However, G9a knockdown synergizes with pharmacologic inhibition of DNMTs resulting in increased hypomethylation and inhibition of cell proliferation. Conclusions: Taken together, these data suggest that G9a is not involved in maintenance of DNA methylation in somatic cells but might play a role in re-initiation of de novo methylation after treatment with hypomethylating drugs, thus serving as a potential target for combinatorial treatments strategies involving DNMTs inhibitors. http://www.epigeneticsandchromatin.com/content/5/1/3 Shikhar Sharma Daniel Gerke Han Han Shinwu Jeong Michael Stallcup Peter Jones Gangning Liang Epigenetics & Chromatin 2012, null:3 2012-01-27T00:00:00Z doi:10.1186/1756-8935-5-3 /content/figures/1756-8935-5-3-toc.gif Epigenetics & Chromatin 1756-8935 ${item.volume} 3 2012-01-27T00:00:00Z PDF Background: The tumor suppressor menin (MEN1) is mutated in the inherited disease multiple endocrine neoplasia type I, and has several documented cellular roles, including the activation and repression of transcription effected by several transcription factors. As an activator, MEN1 is a component of the Set1-like mixed lineage leukemia (MLL) MLL1/MLL2 methyltransferase complex that methylates histone H3 lysine 4 (H3K4). MEN1 is localized to the signal transducer and activator of transcription 1 (STAT1)-dependent gene, interferon regulatory factor 1 (IRF1), and is further recruited when IRF1 transcription is triggered by interferon-γ signaling. Results: RNAi-mediated knockdown of MEN1 alters the H3K4 dimethylation and H3 acetylation profiles, and the localization of histone deacetylase 3, at IRF1. While MEN1 knockdown does not impact the rate of transcription, IRF1 heteronuclear transcripts become enriched in MEN1-depleted cells. The processed mRNA and translated protein product are concomitantly reduced, and the antiviral state is attenuated. Additionally, the transcription start site at the IRF1 promoter is disrupted in the MEN1-depleted cells. The H3K4 demethylase, lysine specific demethylase 1, is also associated with IRF1, and its inhibition alters H3K4 methylation and disrupts the transcription start site as well. Conclusions: Taken together, the data indicate that MEN1 contributes to STAT1-activated gene expression in a novel manner that includes defining the transcription start site and RNA processing. http://www.epigeneticsandchromatin.com/content/5/1/2 Lauren Auriemma Shaili Shah Lara Linden Melissa Henriksen Epigenetics & Chromatin 2012, null:2 2012-01-12T00:00:00Z doi:10.1186/1756-8935-5-2 /content/figures/1756-8935-5-2-toc.gif Epigenetics & Chromatin 1756-8935 ${item.volume} 2 2012-01-12T00:00:00Z XML Regulatory DNA elements such as enhancers, silencers and insulators are embedded in metazoan genomes, and they control gene expression during development. Although they fulfil different roles, they share specific properties. Herein we discuss some examples and a parsimonious model for their function is proposed. All are transcription units that tether their target promoters close to, or distant from, transcriptional hot spots (or 'factories'). http://www.epigeneticsandchromatin.com/content/5/1/1 Petros Kolovos Tobias Knoch Frank Grosveld Peter Cook Argyris Papantonis Epigenetics & Chromatin 2012, null:1 2012-01-09T00:00:00Z doi:10.1186/1756-8935-5-1 /content/figures/1756-8935-5-1-toc.gif Epigenetics & Chromatin 1756-8935 ${item.volume} 1 2012-01-09T00:00:00Z XML Background: Gene regulation in eukaryotes is a complex process entailing the establishment of transcriptionally silent chromatin domains interspersed with regions of active transcription. Imprinted domains consist of clusters of genes, some of which exhibit parent-of-origin dependent monoallelic expression, while others are biallelic. The Kcnq1 imprinted domain illustrates the complexities of long-range regulation that coexists with local exceptions. A paternally expressed repressive non-coding RNA, Kcnq1ot1, regulates a domain of up to 750 kb, encompassing 14 genes. We study how the Kcnq1 gene, initially silenced by Kcnq1ot1, undergoes tissue-specific escape from imprinting during development. Specifically, we uncover the role of chromosome conformation during these events. Results: We show that Kcnq1 transitions from monoallelic to biallelic expression during mid gestation in the developing heart. This transition is not associated with the loss of methylation on the Kcnq1 promoter. However, by exploiting chromosome conformation capture (3C) technology, we find tissue-specific and stage-specific chromatin loops between the Kcnq1 promoter and newly identified DNA regulatory elements. These regulatory elements showed in vitro activity in a luciferase assay and in vivo activity in transgenic embryos. Conclusions: By exploring the spatial organization of the Kcnq1 locus, our results reveal a novel mechanism by which local activation of genes can override the regional silencing effects of non-coding RNAs. http://www.epigeneticsandchromatin.com/content/4/1/21 Lisa Korostowski Anjali Raval Gillian Breuer Nora Engel Epigenetics & Chromatin 2011, null:21 2011-11-15T00:00:00Z doi:10.1186/1756-8935-4-21 /content/figures/1756-8935-4-21-toc.gif Epigenetics & Chromatin 1756-8935 ${item.volume} 21 2011-11-15T00:00:00Z XML Background: A proposed role for Myc in maintaining mouse embryonic stem (ES) cell pluripotency is transcriptional repression of key differentiation-promoting genes, but detail of the mechanism has remained an important open topic. Results: To test the hypothesis that the zinc finger protein Miz-1 plays a central role, in the present work we conducted chromatin immunoprecipitation/microarray (ChIP-chip) analysis of Myc and Miz-1 in human ES cells, finding homeobox (Hox) genes as the most significant functional class of Miz-1 direct targets. Miz-1 differentiation-associated target genes specifically lack acetylated lysine 9 and trimethylated lysine 4 of histone H3 (AcH3K9 and H3K4me3) 9 histone marks, consistent with a repressed transcriptional state. Almost 30% of Miz-1 targets are also bound by Myc and these cobound genes are mostly factors that promote differentiation including Hox genes. Knockdown of Myc increased expression of differentiation genes directly bound by Myc and Miz-1, while a subset of the same genes is downregulated by Miz-1 loss-of-function. Myc and Miz-1 proteins interact with each other and associate with several corepressor factors in ES cells, suggesting a mechanism of repression of differentiation genes. Conclusions: Taken together our data indicate that Miz-1 and Myc maintain human ES cell pluripotency by coordinately suppressing differentiation genes, particularly Hox genes. These data also support a new model of how Myc and Miz-1 function on chromatin. http://www.epigeneticsandchromatin.com/content/4/1/20 Natalia Varlakhanova Rebecca Cotterman Keith Bradnam Ian Korf Paul Knoepfler Epigenetics & Chromatin 2011, null:20 2011-11-04T00:00:00Z doi:10.1186/1756-8935-4-20 /content/figures/1756-8935-4-20-toc.gif Epigenetics & Chromatin 1756-8935 ${item.volume} 20 2011-11-04T00:00:00Z XML Background: Signaling via protein lysine methylation has been proposed to play a central role in the regulation of many physiologic and pathologic programs. In contrast to other post-translational modifications such as phosphorylation, proteome-wide approaches to investigate lysine methylation networks do not exist. Results: In the current study, we used the ProtoArray® platform, containing over 9,500 human proteins, and developed and optimized a system for proteome-wide identification of novel methylation events catalyzed by the protein lysine methyltransferase (PKMT) SETD6. This enzyme had previously been shown to methylate the transcription factor RelA, but it was not known whether SETD6 had other substrates. By using two independent detection approaches, we identified novel candidate substrates for SETD6, and verified that all targets tested in vitro and in cells were genuine substrates. Conclusions: We describe a novel proteome-wide methodology for the identification of new PKMT substrates. This technological advance may lead to a better understanding of the enzymatic activity and substrate specificity of the large number (more than 50) PKMTs present in the human proteome, most of which are uncharacterized. http://www.epigeneticsandchromatin.com/content/4/1/19 Dan Levy Chih Liu Ze Yang Aaron Newman Ash Alizadeh Paul Utz Or Gozani Epigenetics & Chromatin 2011, null:19 2011-10-24T00:00:00Z doi:10.1186/1756-8935-4-19 /content/figures/1756-8935-4-19-toc.gif Epigenetics & Chromatin 1756-8935 ${item.volume} 19 2011-10-24T00:00:00Z XML Background: Histone methylation is regulated by a large number of histone methyltransferases and demethylases. The recently discovered SMCX/KMD5C demethylase has been shown to remove methyl residues from lysine 4 of histone H3 (H3K4), and constitutes an important component of the regulatory element-1-silencing transcription factor (REST) protein complex. However, little is known about the cellular mechanisms that control SMCX activity and intracellular trafficking. Results: In this study, we found that small interfering RNA-mediated knockdown of proliferating cell nuclear antigen (PCNA) resulted in the reduction of the chromatin-bound SMCX fraction. We identified a PCNA-interaction protein motif (PIP box) in the SMCX protein. Using site-directed mutagenesis, we found that the amino acids of the SMCX PIP box are involved in the association of SMCX with PCNA and its interaction with chromatin. Conclusions: Our data indicate that the intracellular trafficking of SMCX is controlled by its association with PCNA. http://www.epigeneticsandchromatin.com/content/4/1/18 Zhihui Liang Marc Diamond Johanna Smith Matthias Schnell Rene Daniel Epigenetics & Chromatin 2011, null:18 2011-10-13T00:00:00Z doi:10.1186/1756-8935-4-18 /content/figures/1756-8935-4-18-toc.gif Epigenetics & Chromatin 1756-8935 ${item.volume} 18 2011-10-13T00:00:00Z XML Background: Expression of Xist, the master regulator of X chromosome inactivation, is extinguished in pluripotent cells, a process that has been linked to programmed X chromosome reactivation. The key pluripotency transcription factors Nanog, Oct4 and Sox2 are implicated in Xist gene extinction, at least in part through binding to an element located in Xist intron 1. Other pathways, notably repression by the antisense RNA Tsix, may also be involved. Results: Here we employ a transgene strategy to test the role of the intron 1 element and Tsix in repressing Xist in ES cells. We find that deletion of the intron 1 element causes a small increase in Xist expression and that simultaneous deletion of the antisense regulator Tsix enhances this effect. Conclusion: We conclude that Tsix and pluripotency factors act synergistically to repress Xist in undifferentiated embryonic stem cells. Double mutants do not exhibit maximal levels of Xist expression, indicating that other pathways also play a role. http://www.epigeneticsandchromatin.com/content/4/1/17 Tatyana Nesterova Claire Senner Janina Schneider Tilly Alcayna-Stevens Anna Tattermusch Myriam Hemberger Neil Brockdorff Epigenetics & Chromatin 2011, null:17 2011-10-07T00:00:00Z doi:10.1186/1756-8935-4-17 /content/figures/1756-8935-4-17-toc.gif Epigenetics & Chromatin 1756-8935 ${item.volume} 17 2011-10-07T00:00:00Z XML Background: Polycomb group (PcG) genes code for chromatin multiprotein complexes that are responsible for maintaining gene silencing of transcriptional programs during differentiation and in adult tissues. Despite the large amount of information on PcG function during development and cell identity homeostasis, little is known regarding the dynamics of PcG complexes and their role during terminal differentiation. Results: We show that two distinct polycomb repressive complex (PRC)2 complexes contribute to skeletal muscle cell differentiation: the PRC2-Ezh2 complex, which is bound to the myogenin (MyoG) promoter and muscle creatine kinase (mCK) enhancer in proliferating myoblasts, and the PRC2-Ezh1 complex, which replaces PRC2-Ezh2 on MyoG promoter in post-mitotic myotubes. Interestingly, the opposing dynamics of PRC2-Ezh2 and PRC2-Ezh1 at these muscle regulatory regions is differentially regulated at the chromatin level by Msk1 dependent methyl/phospho switch mechanism involving phosphorylation of serine 28 of the H3 histone (H3S28ph). While Msk1/H3S28ph is critical for the displacement of the PRC2-Ezh2 complex, this pathway does not influence the binding of PRC2-Ezh1 on the chromatin. Importantly, depletion of Ezh1 impairs muscle differentiation and the chromatin recruitment of MyoD to the MyoG promoter in differentiating myotubes. We propose that PRC2-Ezh1 is necessary for controlling the proper timing of MyoG transcriptional activation and thus, in contrast to PRC2-Ezh2, is required for myogenic differentiation. Conclusions: Our data reveal another important layer of epigenetic control orchestrating skeletal muscle cell terminal differentiation, and introduce a novel function of the PRC2-Ezh1 complex in promoter setting. http://www.epigeneticsandchromatin.com/content/4/1/16 Lovorka Stojic Zuzana Jasencakova Carolina Prezioso Alexandra Stutzer Beatrice Bodega Diego Pasini Rebecca Klingberg Chiara Mozzetta Raphael Margueron Pier Lorenzo Puri Dirk Schwarzer Kristian Helin Wolfgang Fischle Valerio Orlando Epigenetics & Chromatin 2011, null:16 2011-09-05T00:00:00Z doi:10.1186/1756-8935-4-16 /content/figures/1756-8935-4-16-toc.gif Epigenetics & Chromatin 1756-8935 ${item.volume} 16 2011-09-05T00:00:00Z XML