Poly(ADP-ribose) Polymerase 1 Is Inhibited by a Histone H2A Variant, MacroH2A, and Contributes to Silencing of the Inactive X Chromosome

Laval University, Quebec City, Quebec, Canada
Journal of Biological Chemistry (Impact Factor: 4.57). 05/2007; 282(17):12851-9. DOI: 10.1074/jbc.M610502200
Source: PubMed


Poly(ADP-ribose) polymerase 1 (PARP-1) is a nuclear enzyme that is involved in modulating chromatin structure, regulation
of gene expression, and sensing DNA damage. Here, we report that PARP-1 enzymatic activity is inhibited by macroH2A, a vertebrate
histone H2A variant that is enriched on facultative heterochromatin. MacroH2A family members have a large C-terminal non-histone
domain (NHD) and H2A-like histone domain. MacroH2A1.2 and PARP-1 interact in vivo and in vitro via the NHD. The NHD of each macroH2A family member was sufficient to inhibit PARP-1 enzymatic activity in vitro. The NHD of macroH2A1.2 was a mixed inhibitor of PARP-1 catalytic activity, with affects on both catalytic activity and the
substrate binding affinity of PARP-1. Depletion of PARP-1 by RNA interference caused reactivation of a reporter gene on the
inactive X chromosome, demonstrating that PARP-1 participates in the maintenance of silencing. These results suggest that
one function of macroH2A in gene silencing is to inhibit PARP-1 enzymatic activity, and this may affect PARP-1 association
with chromatin.

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Available from: Dmitri A Nusinow, Nov 19, 2015
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    • "In contrast, the maintenance phase of XCI is characterized by almost complete resistance of the Xi to reactivation upon Xist deletion [19,20]. To explain this switch in Xist dependence with XCI phase, studies in differentiated female cells have described synergism between Xist RNA, DNA methylation, histone variants, and histone hypoacetylation in maintaining XCI [20-22]. For instance, assaying primary mouse embryonic fibroblasts (MEFs) harboring a GFP reporter on the Xi that is subject to X-inactivation, showed reactivation in approximately 11% of cells 13 days after simultaneous deletion of Xist and Dnmt1[20]. "
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    ABSTRACT: Background X chromosome inactivation (XCI) is a developmental program of heterochromatin formation that initiates during early female mammalian embryonic development and is maintained through a lifetime of cell divisions in somatic cells. Despite identification of the crucial long non-coding RNA Xist and involvement of specific chromatin modifiers in the establishment and maintenance of the heterochromatin of the inactive X chromosome (Xi), interference with known pathways only partially reactivates the Xi once silencing has been established. Here, we studied ATF7IP (MCAF1), a protein previously characterized to coordinate DNA methylation and histone H3K9 methylation through interactions with the methyl-DNA binding protein MBD1 and the histone H3K9 methyltransferase SETDB1, as a candidate maintenance factor of the Xi. Results We found that siRNA-mediated knockdown of Atf7ip in mouse embryonic fibroblasts (MEFs) induces the activation of silenced reporter genes on the Xi in a low number of cells. Additional inhibition of two pathways known to contribute to Xi maintenance, DNA methylation and Xist RNA coating of the X chromosome, strongly increased the number of cells expressing Xi-linked genes upon Atf7ip knockdown. Despite its functional importance in Xi maintenance, ATF7IP does not accumulate on the Xi in MEFs or differentiating mouse embryonic stem cells. However, we found that depletion of two known repressive biochemical interactors of ATF7IP, MBD1 and SETDB1, but not of other unrelated H3K9 methyltransferases, also induces the activation of an Xi-linked reporter in MEFs. Conclusions Together, these data indicate that Atf7ip acts in a synergistic fashion with DNA methylation and Xist RNA to maintain the silent state of the Xi in somatic cells, and that Mbd1 and Setdb1, similar to Atf7ip, play a functional role in Xi silencing. We therefore propose that ATF7IP links DNA methylation on the Xi to SETDB1-mediated H3K9 trimethylation via its interaction with MBD1, and that this function is a crucial feature of the stable silencing of the Xi in female mammalian cells.
    Full-text · Article · Jun 2014 · Epigenetics & Chromatin
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    • "PARP1 belongs to a group of nucleosome binding proteins that affect chromatin structure, and, when catalytically inactive, it inhibits transcription by binding to chromatin. macroH2A may therefore act as a transcriptional silencer by associating with PARP1 to repress its enzymatic activity through the macro domain (Ouararhni et al., 2006; Nusinow et al., 2007). However, targeted disruption of H2afy and Parp1 in mice revealed that mutants homozygous for either gene are viable and fertile, demonstrating their nonessential roles in chromatin regulation during normal development (Wang et al., 1995; Changolkar et al., 2007). "
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    ABSTRACT: X chromosome inactivation (X-inactivation) is triggered by X-linked noncoding Xist RNA, which is expressed asymmetrically from one of the two X chromosomes in females and coats it in cis to induce chromosome-wide silencing. Xist RNA is thought to play a role as a platform in recruiting proteins involved in gene silencing and heterochromatinization, which mediate serial changes in epigenetic modification of the chromatin. During the last two decades, many proteins have been shown to be enriched on the inactivated X chromosome in mouse and human. Although the biological significance of most of them for X-inactivation has not been fully established, extensive studies of these proteins should provide a better understanding of the molecular basis of how X-inactivation mediated by Xist RNA is regulated. Here, we review the potential roles of some of these proteins in the stepwise process of Xist RNA-mediated chromosome silencing.
    Full-text · Article · Jan 2014 · Genes & Genetic Systems
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    • "PARP1 is typically associated with active promoters, where it replaces the linker histone H1 and catalyzes the transfer of ADP-ribose units to target proteins, including itself, leading to its release from chromatin. The globular domain of macroH2A inhibits this catalytic activity (Ouararhni et al., 2006;Nusinow et al., 2007). In the catalytically inactive state, extensive PARP1 binding has been shown to repress gene expression, perhaps through dimerization, suggesting that macroH2A might recruit PARP1 to the Xi and then inhibit PARP1 catalytic activity in order to retain a high density of PARP1 binding (Wacker et al., 2007). "
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    ABSTRACT: Most histones are assembled into nucleosomes during replication to package genomic DNA. However, several variant histones are deposited independently of replication at particular regions of chromosomes. Such histone variants include cenH3, which forms the nucleosomal foundation for the centromere, and H3.3, which replaces histones that are lost during dynamic processes that disrupt nucleosomes. Furthermore, various H2A variants participate in DNA repair, gene regulation and other processes that are, as yet, not fully understood. Here, we review recent studies that have implicated histone variants in maintaining pluripotency and as causal factors in cancer and other diseases.
    Preview · Article · Jun 2013 · Development
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