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Functional Dissection of Variant Polycomb Repressive Complex 1 Subunits RYBP and YAF2 during Neural Differentiation of Embryonic Stem Cells [ChIP-Seq]

ABSTRACT: Chromatin immunoprecipitation sequencing (ChIP-seq) for RING1B, RYBP, YAF2, PRC2 complex (EZH2, MTF2 and JARID2) as well as the histone modifications H2AK119ub, H3K27me3 and H3K27ac in mESCs and the neural differentiated cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE213414 | GEO | 2023/10/09

REPOSITORIES: GEO

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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

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

Gene expression profile in Yaf2 KD and/or RYBP KO ES cells.

Project description:Gene expression change by Yaf2 KD in wild type or RYBP KO ES cells.

2012-04-04 | GSE32288 | GEO

Gene expression profile in Yaf2 KD and/or RYBP KO ES cells.

Project description:Gene expression change by Yaf2 KD in wild type or RYBP KO ES cells. Total RNAs were extracted from the respective ES cells, and were subjected to microarray analysis using Affymetrix GeneChip Mouse Genome 430A 2.0 arrays

2012-04-03 | E-GEOD-32288 | biostudies-arrayexpress

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

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

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

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 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.

2012-02-09 | GSE34774 | GEO

Functional Dissection of Variant Polycomb Repressive Complex 1 Subunits RYBP and YAF2 during Neural Differentiation of Embryonic Stem Cells [ATAC-Seq]

Project description:ATAC-seq was used to investigate the impact of Rybp knockout on chromatin accessibility in 46C mESCs.

2023-10-09 | GSE213415 | GEO

Elucidation of BMI1, RYBP and H2AK119ub interactomes in Glioblastoma

Project description:Identification of BMI1, RYBP and H2AK119UB interactome in Glioblastoma (GBM) to elucidate BMI1 roles independent of the PRC1-complex in GBM.

2021-09-09 | PXD022057 | Pride

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