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PCGF Homologs and RYBP Define Functionally Distinct PRC1 Family Complexes

ABSTRACT: The heterogeneous nature of mammalian PRC1 complexes has hindered our understanding of their biological functions. Here, we present a comprehensive proteomic and genomic analysis that uncovered six major groups of PRC1 complexes each containing a distinct PCGF subunit, a RING1A/B ubiquitin ligase, and a unique set of associated polypeptides. These PRC1 complexes differ in their genomic localization and only a small subset co-localize with H3K27me3. Further biochemical dissection revealed that the six PCGF–RING1A/B combinations form multiple complexes through association with RYBP or its homolog YAF2, which prevents the incorporation of other canonical PRC1 subunits such as CBX, PHC and SCM. Although both RYBP/YAF2- and CBX/PHC/SCM-containing complexes compact chromatin, only RYBP stimulates the activity of RING1B toward H2AK119ub1, suggesting a central role in PRC1 function. Knockdown of RYBP in ES cells compromised their ability to form embryoid bodies, likely because of defects in cell proliferation and maintenance of H2AK119ub1 level.

ORGANISM(S): Homo sapiens

PROVIDER: GSE34774 | GEO | 2012/02/09

SECONDARY ACCESSION(S): PRJNA150339

REPOSITORIES: GEO

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PCGF Homologs and RYBP Define Functionally Distinct PRC1 Family Complexes

Project description:The heterogeneous nature of mammalian PRC1 complexes has hindered our understanding of their biological functions. Here, we present a comprehensive proteomic and genomic analysis that uncovered six major groups of PRC1 complexes each containing a distinct PCGF subunit, a RING1A/B ubiquitin ligase, and a unique set of associated polypeptides. These PRC1 complexes differ in their genomic localization and only a small subset co-localize with H3K27me3. Further biochemical dissection revealed that the six PCGFM-bM-^@M-^SRING1A/B combinations form multiple complexes through association with RYBP or its homolog YAF2, which prevents the incorporation of other canonical PRC1 subunits such as CBX, PHC and SCM. Although both RYBP/YAF2- and CBX/PHC/SCM-containing complexes compact chromatin, only RYBP stimulates the activity of RING1B toward H2AK119ub1, suggesting a central role in PRC1 function. Knockdown of RYBP in ES cells compromised their ability to form embryoid bodies, likely because of defects in cell proliferation and maintenance of H2AK119ub1 level. ChIP-seq experiments of different PRC1 components were performed either on HA-tagged transgenic stable 293T-REx lines or on endogenous subunits using specific antibodies.

2012-02-09 | E-GEOD-34774 | biostudies-arrayexpress

Functional Dissection of Variant Polycomb Repressive Complex 1 Subunits RYBP and YAF2 during Neural Differentiation of Embryonic Stem Cells

Project description:Polycomb repressive complex 1 (PRC1) comprises two different complexes: CBX-containing canonical PRC1 (cPRC1) and RYBP/YAF2-containing variant PRC1 (vPRC1). RYBP-vPRC1 or YAF2-vPRC1 catalyzes H2AK119ub through a positive-feedback model; however, whether RYBP and YAF2 have different regulatory functions is still unclear. Here, we show that the expression of RYBP and YAF2 decreases and increases, respectively, during neural differentiation of embryonic stem cells (ESCs). Rybp knockout impairs neural differentiation by activating Wnt signaling and derepressing nonneuroectoderm-associated genes. However, Yaf2 knockout promotes neural differentiation and leads to redistribution of RYBP binding, increases enrichment of RYBP and H2AK119ub on the RYBP-YAF2 cotargeted genes, and prevents ectopic derepression of nonneuroectoderm-associated genes in neural-differentiated cells. Taken together, this study reveals that RYBP and YAF2 function differentially in regulating mESC neural differentiation.

2023-10-07 | GSE213416 | GEO

Functional dissection of PRC1 subunits RYBP and YAF2 during neural differentiation of embryonic stem cells

Project description:Polycomb repressive complex 1 (PRC1) comprises two different complexes: CBX-containing canonical PRC1 (cPRC1) and RYBP/YAF2-containing variant PRC1 (vPRC1). RYBP and its paralog YAF2 recruit vPRC1 to catalyze H2AK119ub through a positive-feedback model. Here, we show that expression of RYBP and YAF2 decreases and increases, respectively, during neural differentiation of embryonic stem cells (ESCs). Rybp knockout impairs neural differentiation by activating Wnt signaling and derepressing nonneuroectoderm-associated genes. However, Yaf2 knockout promotes neural differentiation and leads to redistribution of RYBP binding, increases enrichment of RYBP and H2AK119ub on the RYBP-YAF2 co-targeted genes, and prevents ectopic derepression of nonneuroectoderm-associated genes in neural-differentiated cells. Furthermore, the phase separations mediated by RYBP alone or together with RING1B are easier and more stable than those by YAF2, which might facilitate the deposition of H2AK119ub more abundantly by RYBP-PRC1 than YAF2-PRC1. Together, this study reveals that RYBP might maintain repressed chromatin more strongly and function differentially in regulating mESC neural differentiation compared with YAF2.

2023-10-09 | GSE213413 | GEO

RBYP stimulates PRC1 to shape chromatin-based communication between polycomb repressive complexes [RNA-seq]

Project description:Polycomb Repressive Complexes (PRC), and their chromatin-modifying activities, are essential for the correct regulation of gene expression during cellular differentiation and development. Although their role in transcriptional repression is well described, a detailed molecular understanding of their complex assembly and enzymatic activity has been lacking. We therefore set out to characterize the relationship between PRC1 complex composition and its ability to catalyse H2AK119ub1 for one of the most abundant PRC1 complexes in embryonic stem cells, PCGF1-PRC1. Biochemical reconstitution of the PCGF1-PRC1 complex revealed that RYBP/YAF2 was essential for robust enzymatic activity of the complex. Using calibrated ChIP-seq for H2AK119ub1, we identify that RYBP-dependent PRC1 activity has a widespread role in shaping H2AK119ub1 levels genome-wide in mouse embryonic stem cells. Furthermore, these H2AK119ub1 levels stimulate PRC2 activity as part of an activity-based feedback loop, which we demonstrate is required for maintenance of transcriptional repression. Together, these observations uncover complex-based principles for PRC1 assembly and activity, and further our understanding of Polycomb domain function.

2016-10-05 | GSE83134 | GEO

RBYP stimulates PRC1 to shape chromatin-based communication between polycomb repressive complexes [ChIP-seq]

2016-10-05 | GSE83094 | GEO

RBYP stimulates PRC1 to shape chromatin-based communication between polycomb repressive complexes

2016-10-05 | GSE83135 | GEO

RBYP stimulates PRC1 to shape chromatin-based communication between polycomb repressive complexes [calChIP-seq]

2016-10-05 | GSE83093 | GEO

Expression regulation by Yaf2 in mouse embryonic stem cells

Project description:The Polycomb group (PcG) proteins are the key epigenetic regulators with well-established roles in stem cell maintenance. To date, biochemical analyses have identified noncanonical PRC1(nc-PRC1) complexes characterized by the presence of Rybp/Yaf2 and the lack of CBX proteins. The biological significance of these nc-PRC1s and the potential mechanisms by which they mediate gene repression are largely unknown. Here we show that disruption of Yaf2 results in compromised proliferation and abnormal differentiation in mouse embryonic stem cells (mESCs). Deletion analysis identifies the region encompassing amino acid residues 102–150 required for the assembly of Yaf2 into nc-PRC1 complexes. Furthermore, we found that substitution of serine 166 by alanine (S166A) caused a loss of Yaf2-phosphorylation signal in mESCs. Loss of such Yaf2-phosphorylation compromises Ring1B-mediated H2A monoubiquitination and in turn lose its ability to repress target gene expression. We therefore propose that Yaf2 phosphorylation enhances its ability to maintain the pluripotent state in mESCs.

2018-08-30 | GSE113830 | GEO

Expression regulation by RYBP in mouse embryonic stem cells

Project description:Polycomb repressive complexes (PRCs) are important chromatin regulators of ES cell function. RYBP binds Polycomb H2A monoubiquitin ligases Ring1A and Ring1B, and has been suggested to participate in localizing Polycomb complexes to their targets. Moreover, constitutive inactivation of RYBP precludes ES cell formation. Here we have used ES cells conditionally deficient in RYBP to investigate RYBP function. Chromosome immunoprecipitation on a chip (ChIP-chip) of RYBP and microarray experiments were performed using wild type and knocked-out ES cells. Gene expression profiling of WT, conditionally deficient in RYBP with or without Yaf2 RNAi, and ChIP-chip of RYBP on promoters of WT, Dnmt1-KO or Eed-KO ES cells.

2012-04-03 | E-GEOD-32294 | biostudies-arrayexpress

PCGF5 is required for neural differentiation of embryonic stem cells [ChIP-seq]

Project description:Polycomb-group proteins are key regulators of the transcriptional programs that maintain stem cell identity and dictate lineage specification. Polycomb repressor complex 1 (PRC1) contains the E3 ligases RING1A/B, which monoubiquitinate lysine 119 at histone H2A (H2AK119ub1) to regulate gene expression. PRC1 has been sub-classified into six major complexes based on the presence of a PCGF subunit. Here, we find that Pcgf5, one of six PCGF paralogs, is an important requirement in the differentiation of mouse embryonic stem cells (mESCs) towards a neural cell fate. Although PCGF5 is not required for mESC self-renewal, its loss blocks mESC neural differentiation by activating the SMAD2/TGF-β signaling pathway. Inhibition of SMAD2/TGF-β signaling or rescue by overexpression of Pcgf5 can restore the capability of mESCs to differentiate towards a neural cell fate. PCGF5 works by stimulating RING1B-dependent H2AK119ub1 both in vitro and in vivo, leading to the suppression of TGF-β signaling genes. PCGF5 loss-of-function prevents the reduction of H2AK119ub1 and H3K27me3 around neural specific genes and keeps them repressed. Our results showed that PCGF5 might function as both a repressor for SMAD2/TGF-β signaling pathway and a facilitator for neural differentiation. Together, our findings reveal a critical context-specific function for PCGF5 in directing PRC1 to control cell fate.

2018-03-10 | GSE107377 | GEO

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