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Variant PCGF1-PRC1 links PRC2 recruitment with induced transcriptional inactivation at target genes [CUT&Tag]

ABSTRACT: Polycomb repressive complexes-1 and -2 (PRC1 and 2), silence developmental genes in spatiotemporally regulated manner during metazoan embryogenesis. How PcG proteins contribute to down-regulation of target genes upon differentiation, however, remains elusive. Here, by differentiating embryonic stem cells into embryoid bodies, we reveal a crucial role of a PCGF1 (Polycomb group RING finger protein 1)-containing variant PRC1 complex (PCGF1-PRC1) to facilitate induced down-regulation of a group of genes. Binding of PCGF1-PRC1 results in down-regulation of transcriptional activity, followed by Histone H2AK119 mono-ubiquitination (H2AK119ub1) and subsequent recruitment of PRC2, to initiate PcG-repressive domain formation. Based on these findings, we propose that PCGF1-PRC1 mediates establishment of PcG-repressive domains at target genes during differentiation.

ORGANISM(S): Mus musculus

PROVIDER: GSE141486 | GEO | 2021/05/31

REPOSITORIES: GEO

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Variant PCGF1-PRC1 links PRC2 recruitment with induced transcriptional inactivation at target genes [ChIP-seq]

Project description:Polycomb repressive complexes-1 and -2 (PRC1 and 2), silence developmental genes in spatiotemporally regulated manner during metazoan embryogenesis. How PcG proteins contribute to down-regulation of target genes upon differentiation, however, remains elusive. Here, by differentiating embryonic stem cells into embryoid bodies, we reveal a crucial role of a PCGF1 (Polycomb group RING finger protein 1)-containing variant PRC1 complex (PCGF1-PRC1) to facilitate induced down-regulation of a group of genes. Binding of PCGF1-PRC1 results in down-regulation of transcriptional activity, followed by Histone H2AK119 mono-ubiquitination (H2AK119ub1) and subsequent recruitment of PRC2, to initiate PcG-repressive domain formation. Based on these findings, we propose that PCGF1-PRC1 mediates establishment of PcG-repressive domains at target genes during differentiation.

2021-05-31 | GSE141485 | GEO

Variant PCGF1-PRC1 links PRC2 recruitment with induced transcriptional inactivation at target genes [RNA-seq]

2021-05-31 | GSE141487 | GEO

PCGF1-PRC1 links chromatin repression with DNA replication during hematopoietic cell lineage commitment

Project description:Polycomb repressive complexes 1 and 2 (PRC1 and 2) repress lineage inappropriate genes during development to maintain proper cellular identities. To reveal the function of a variant PRC1 containing PCGF1 (PCGF1-PRC1), we prepared PCGF1 interacting proteins by immunoprecipitation and characterized them by LC-MS/MS.

2022-11-30 | PXD036330 | Pride

Gene regulation by PCGF1 in hematopoietic progenitor cells

Project description:Polycomb group proteins (PcG), namely polycomb repressive complexes 1 and 2 (PRC1 and 2), repress lineage inappropriate genes during development to maintain proper cellular identities. It has been recognized that PRC1 localizes at replication fork, however, the precise functions of PRC1 during DNA replication are elusive. In this study, to elucidate the role of PCGF1 in the fork we’ve examined nucleosome occupancy at the fork by iPOND-MNase seq. In addition we’ve examined the biological relevancy by performing single cell RNA-seq derived Pcgf1 deficient hematopoietic progenitor cells to describe how cellular fate is affected by the impact of PCGF1 on nascent nucleosome configuration.

2022-10-19 | GSE166171 | GEO

PR-DUB safeguards Polycomb repression through restricting H2AK119ub1 [RNA-seq]

Project description:Polycomb group (PcG) proteins are critical chromatin regulators for cell fate control. The mono-ubiquitylation on histone H2AK119 (H2AK119ub1) is one of the well-recognized mechanisms for Polycomb Repressive Complex 1 (PRC1)-mediated transcription repression. However, the specific H2AK119 deubiquitylation complex composed by ASX-like proteins (ASXLs) and BAP1 has also been genetically characterized as a Polycomb Repressive complex (PR-DUB). Here we try to provide a rationale for these counterintuitive findings. Through re-examining the genomic distribution of H2AK119ub1, we find that H2AK119ub1 is non-negligibly distributed at non-promoter regions and associated with PRC1 sampling. Upon deletion of Asxl2 in mouse embryonic stem cells (ESCs), H2AK119ub1 is pervasively gained, especially at non-promoter regions, which is associated with increased RING1B occupancy. Meanwhile RING1B is significantly lost from a subset of the target promoters and thereby results in minor derepression in Asxl2-null ESCs. However notably, Asxl2 loss causes aberrant lineage differetiation, similar to PcG mutants. Therefore, our data reconcile seemingly paradoxical roles of PR-DUB on transcription repression and highlight the importance of a balanced H2AK119ub1 dynamics in developmental regulation.

2023-03-31 | GSE186374 | GEO

PR-DUB safeguards Polycomb repression through restricting H2AK119ub1 [ChIP-seq]

2023-03-31 | GSE186373 | GEO

PCGF1-PRC1 safeguards recovery of nucleosome positioning during S-phase to ensure early hematopoiesis

2023-05-13 | PXD033883 | JPOST Repository

Expression regulation by Pcgf1 in mouse embryonic stem cells

Project description:The Polycomb repressive complex 1 (PRC1) is essential for fate decisions of embryonic stem (ES) cells. Emerging evidence suggests that six major variants of PRC1 complex, defined by the mutually exclusive presence of Pcgf subunit, regulate distinct biological processes, yet very little is known about the mechanism by which each version of PRC1 instructs and maintains cell fate. Here, we disrupted the Pcgf1, also known as Nspc1 and one of six Pcgf paralogs, in mouse ES cells by the CRISPR/Cas9 technology. We showed that although these mutant cells were viable and retained normal self-renewal, they displayed severe defects in differentiation in vitro. To gain a better understanding of the role of Pcgf1 in transcriptional control of differentiation, we analysed mRNA profiles from Pcgf1 deficient cells using RNA-seq. In contrast to the canonical role of PRC1 in gene repression, we found that Pcgf1 mainly functioned as a transcriptional activator to drive expression of many genes involved in ectoderm and mesoderm differentiation. Chromatin immunoprecipitation experiments demonstrated that Pcgf1 deletion caused a decrease in Ring1B and its associated H2AK119ub1 mark binding to target genes. Altogether, our results revealed an unexpected function of Pcgf1 in gene activation during ES cell maintenance.

2017-06-13 | GSE95383 | 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]

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