A Novel Mammalian Complex Containing Sin3B Mitigates Histone Acetylation and RNA Polymerase II Progression within Transcribed Loci

Abstract

Transcription requires the progression of RNA polymerase II (RNAP II) through a permissive chromatin structure. Recent studies of Saccharomyces cerevisiae have demonstrated that the yeast Sin3 protein contributes to the restoration of the repressed chromatin structure at actively transcribed loci. Yet, the mechanisms underlying the restoration of the repressive chromatin structure at transcribed loci and its significance in gene expression have not been investigated in mammals. We report here the identification of a mammalian complex containing the corepressor Sin3B, the histone deacetylase HDAC1, Mrg15, and the PHD finger-containing Pf1 and show that this complex plays important roles in regulation of transcription. We demonstrate that this complex localizes at discrete loci approximately 1 kb downstream of the transcription start site of transcribed genes, and this localization requires both Pf1's and Mrg15's interaction with chromatin. Inactivation of this mammalian complex promotes increased RNAP II progression within transcribed regions and subsequent increased transcription. Our results define a novel mammalian complex that contributes to the regulation of transcription and point to divergent uses of the Sin3 protein homologues throughout evolution in the modulation of transcription.Regulation of gene expression impacts virtually all cellular processes and relies primarily on accurate regulation of transcription. It has become increasingly clear that transcription itself is regulated not only at the level of initiation, but also during elongation and termination. While the molecular events underlying transcription initiation have been in part elucidated in the recent past, how transcription elongation and transcription termination modulate gene expression in mammals remains largely elusive.In eukaryotes, the presence of nucleosomes interspersed along the chromatin fiber is believed to represent a major barrier for RNA polymerase II (RNAP II) entry and progression (30). To allow the recruitment of the transcription machinery and transcriptional initiation, the transcriptional start sites (TSS) of active genes are, for the most part, devoid of nucleosomes. In contrast, downstream transcribed regions are tightly packed with nucleosomes, which are likely to prevent aberrant entry of the transcription machinery within coding regions, but they can also hinder progression of the polymerase. In order for RNAP II to progress through the transcribed region, the generation of a permissive chromatin structure is needed and involves the removal and redeposition of nucleosomes along transcribed regions. Such a mechanism is believed to be controlled in part by posttranslational modifications of histones, such as by acetylation and methylation, which are actively involved in regulation of transcriptional elongation (2,18,20). Among these modifications, histone acetylation has long been recognized to be associated with transcriptional activation. However, its function in transcription and its regulation have been studied m...

Senescence-associated SIN3B promotes inflammation and pancreatic cancer progression

“…However, our transcriptomic analysis failed to identify potential intermediate factors that positively regulate Il1a levels, while being repressed by SIN3B. An alternative explanation for this positive regulation of IL-1α by SIN3B may stem from our recent observation that SIN3B participates in the release of polymerase pausing at active promoters, thus modulating the levels of actively transcribed genes (51).…”

Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex

“…1D, lane 2), Sin3 remains associated with the rest of the subunits of Rpd3S. Lastly, Ume1 seems to only contact Sin3, and its absence does not influence other components of Rpd3S, which may explain the fact that no obvious ortholog has been found in flies and mammals (36,37).…”

“…Two key components of Rpd3S that were shown to involve chromatin recognition are Eaf3, which contains a chromodomain (CHD) that binds to H3K36me, and Rco1, which contains two PHD domains with PHD1 being essential for Rpd3S function (11). All Rpd3S complexes that have been reported appear to function at coding regions where H3K36me is enriched, although the functional consequences of the resulting hypoacetylation at coding regions vary among species (22,36,37). We recently showed that Rpd3S prefers dinucleosome substrates and bridges between two linked nucleosomes (38).…”

“…The Rpd3S complex is evolutionarily conserved, and the orthologs of its key subunits can be found in many species including flies and mammals (36,37). The yeast Rpd3S is approximately a 410-kDa complex (38) composed of five subunits.…”

Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex

“…Whereas the larger 1.2-to 2-MDa mammalian Sin3L/Rpd3L complex comprising seven unique subunits and at least as many paralogs is recruited to the promoter regions of genes by sequence-specific DNA-binding transcription factors, the smaller 0.5-to 0.6-MDa Sin3S/Rpd3S complex comprising five unique subunits and at least three paralogs is targeted to the intragenic regions of actively transcribed genes through interactions with specific chromatin signals (9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23). Both complexes share Sin3A/B, HDAC1/2, and RBBP4/7 subunits and rely largely on HDAC activity to affect transcriptional repression; we note that there is now increasing evidence that Sin3A and Sin3B partition into the Sin3L/ Rpd3L and Sin3S/Rpd3S complexes, respectively (20,23).…”