Network of phosphatases and HDAC complexes at repressed chromatin

Abstract

Tight regulation of gene expression is achieved by a variety of protein complexes that selectively bind chromatin, modify it and change its transcription competency. Histone acetylases (HATs) and deacetylases (HDACs) play an important role in this process. They can generate transcriptionally active or inactive chromatin through the addition (HATs) or removal (HDACs) of acetyl groups on histones, respectively.Repo-Man is a Protein Phosphatase 1 targeting subunit that accumulates on chromosomes during mitotic exit and mediates the removal of mitotic histone H3 phosphorylations. It was shown recently that Repo-Man also regulates heterochromatin formation in interphase and that its depletion favours the switch between transcriptionally inactive and active chromatin, demonstrating that its role goes well beyond mitosis.Here, we provide the first link between a phosphatase and HDAC complexes. We show that genome-wide Repo-Man binding sites overlap with chromatin regions bound by members of the three HDAC complexes (Sin3a, NuRD and CoREST). We establish that members of the NuRD and Sin3a HDAC complexes interact with Repo-Man by mass spectrometry and that Repo-Man is in close proximity to SAP18 (Sin3a) in interphase as observed by the Proximity Ligation Assay. Altogether, these data suggest a mechanism by which Repo-Man/PP1 complex, via interactions with HDACs, could stabilise gene repression.

KRCC1: A potential therapeutic target in ovarian cancer

“…Similar to KRCC1, inhibition of HDAC restores epithelial differentiation and abolishes anchorage independent growth in cancer cells . Genome‐wide binding studies have established a link between PP1 phosphatase and HDAC complexes that bind chromatin regions in an overlapping fashion . Moreover, genome‐wide promoter binding studies in HeLa have identified ~500 promoters that bind PP1 .…”

“…[41][42][43] Interestingly like PP1 interacting proteins (PIPs), KRCC1 is intrinsically disordered (Supplementary Figure S8) and specifically associates with the catalytic subunit PP1CC and with HDAC1/2 but not with PP1CA or PP1CB, the other closely related isoforms that are expressed in mammalian cells but differ primarily in their N-and C-termini. 41 While the interaction of PP1CC with HDAC1/2 is well-documented the precise biological implications are emerging 34,35 and suggest regulation of gene transcription 44 and replication stress. 37 Increased acetylation of histone 3/4 and phosphorylation of CHK1 in KRCC1 silenced cells suggest reduced deacetylase and phosphatase activities at these respective sites, which may indicate the inability of PP1CC and HDAC to localize to specific chromatin loci in the absence of KRCC1.…”

“…49 Genome-wide binding studies have established a link between PP1 phosphatase and HDAC complexes that bind chromatin regions in an overlapping fashion. 44 Moreover, genome-wide promoter binding studies in HeLa have identified ~500 promoters that bind PP1. 50 However, the nuclear PIPs, PNUTS, NIPP1, and Repo-Man taken together account for only ~24% overlap with this promoter dataset 50 raising the possibility that a percentage of these and other promoters may be co-occupied and transcriptionally regulated by the KRCC1-PP1CC-HDAC axis ultimately affecting important processes including cellular plasticity.…”

“…Interestingly like PP1 interacting proteins (PIPs), KRCC1 is intrinsically disordered (Supplementary Figure S8) and specifically associates with the catalytic subunit PP1CC and with HDAC1/2 but not with PP1CA or PP1CB, the other closely related isoforms that are expressed in mammalian cells but differ primarily in their N‐ and C‐termini . While the interaction of PP1CC with HDAC1/2 is well‐documented the precise biological implications are emerging and suggest regulation of gene transcription and replication stress …”

Targeting of SET/I2PP2A oncoprotein inhibits Gli1 transcription revealing a new modulator of Hedgehog signaling

“…We tested this hypothesis by analyzing protein interactions of GFP-SET or GFP by immunoprecipitation experiments using the anti-GFP antibody, followed by mass spectrometry (MS) analysis of the immunoprecipitated proteins. This experimental approach identified SAP18 as an interactor of SET, a component of the mSin3 and histone deacetylase complex 48 , 49 that cooperates with Sufu to repress Gli1-mediated transcription 45 , 46 . The MS analysis also revealed two known interactors of SET, glyceraldehyde-3-phosphate dehydrogenase 50 and T-complex protein 1 subunit delta 51 .…”