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

ABSTRACT: 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.

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Haruhiko Koseki

PROVIDER: PXD033883 | JPOST Repository | Sat May 13 00:00:00 BST 2023

REPOSITORIES: jPOST

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Dataset's files

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			Action	DRS
	001_WT1_250ng_T120SW_B3.wiff	Wiff
	001_WT1_250ng_T120SW_B3.wiff.scan	Wiff
	002_Pcgf1-KO1_250ng_T120SW_B3.wiff	Wiff
	002_Pcgf1-KO1_250ng_T120SW_B3.wiff.scan	Wiff
	003_WT2_250ng_T120SW_B3.wiff	Wiff

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Publications

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

Takano Junichiro J Ito Shinsuke S Dong Yixing Y Sharif Jafar J Nakajima-Takagi Yaeko Y Umeyama Taichi T Han Yong-Woon YW Isono Kyoichi K Kondo Takashi T Iizuka Yusuke Y Miyai Tomohiro T Koseki Yoko Y Ikegaya Mika M Sakihara Mizuki M Nakayama Manabu M Ohara Osamu O Hasegawa Yoshinori Y Hashimoto Kosuke K Arner Erik E Klose Robert J RJ Iwama Atsushi A Koseki Haruhiko H Ikawa Tomokatsu T

Nature communications 20221128 1

Polycomb group proteins (PcG), 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 the replication fork, however, the precise functions of PRC1 during DNA replication are elusive. Here, we reveal that a variant PRC1 containing PCGF1 (PCGF1-PRC1) prevents overloading of activators and chromatin remodeling factors on nascent DNA and thereby mediates proper de ...[more]

PMID: 36443290

Similar Datasets

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

USP7 represses lineage differentiation genes in mouse embryonic stem cells by both catalytic and non-catalytic activity

Project description:USP7, a ubiquitin-specific peptidase (USP), plays an important role in many cellular processes through its catalytic deubiquitination of various substrates. However, its nuclear function to shape the transcriptional network in mouse embryonic stem cells (mESCs) remains poorly understood. Here, we report that USP7 maintains mESCs identity through both catalytic activity-dependent and -independent repression of lineage differentiation genes. Usp7 depletion attenuates SOX2 level and derepresses lineage differentiation genes thereby compromising mESCs pluripotency. Mechanistically, USP7 deubiquitinates and stabilizes SOX2 to repress mesoendodermal (ME) lineage genes. Moreover, USP7 assembles into RYBP-variant Polycomb repressive complex 1 and contributes to Polycomb chromatin-mediated repression of ME lineage genes in a catalytic activity-dependent manner. Importantly, USP7 deficient in its deubiquitination function is able to maintain RYBP binding to chromatin for repressing primitive endoderm-associated genes. Overall, our study demonstrates that USP7 harbors both catalytic and non-catalytic activity to repress different lineage differentiation genes thereby revealing a previously unrecognized role in controlling gene expression for maintaining mESCs identity.

2023-07-20 | PXD039633 | Pride

Replication stress impairs CENP-A nucleosome stability in S phase

Project description:MS .raw files for manuscript, "DNA Replication Stress Impairs Proper Centromere Inheritance."

2025-04-02 | MSV000097501 | MassIVE

Crosslinking mass spectrometry of DDM1 complexed with the nucleosome

Project description:DECREASE IN DNA METHYLATION 1 (DDM1) is the chromatin remodeling factor that has been genetically identified in Arabidopsis thaliana as a factor involved in the maintenance of repressive epigenomic modifications over transposons. In this study, we performed crosslinking mass spectrometry and biochemical analysis using reconstituted nucleosome to understand the chromatin remodeling activity of DDM1. We found that the unique C-terminal tail of heterochromain-specific H2A.W variant binds to DDM1. This result suggest that DDM1 functions with specific histone variants for the maintenance of repressive modifications and epigenetic regulation of transposon activity.

2024-05-31 | PXD043417 | JPOST Repository

PRC2 coordinates lineage fidelity and DNA methylation during ESC differentiation (RRBS)

Project description:Polycomb Repressive Complex 2 (PRC2) catalyzes histone H3 lysine 27 tri-methylation, an epigenetic modification associated with gene repression. H3K27me3 is enriched at the promoters of a large cohort of developmental genes in embryonic stem cells (ESCs). Loss of H3K27me3 leads to a failure of ESCs to properly differentiate, which presents a major roadblock for dissecting the precise roles of PRC2 activity during lineage commitment. While recent studies suggest that loss of H3K27me3 leads to changes in DNA methylation in ESCs, how these two pathways coordinate to regulate gene expression programs during lineage commitment is poorly understood. Here, we analyzed gene expression and DNA methylation levels in several PRC2 mutant ESC lines that maintain varying levels of H3K27me3. We found that maintenance of intermediate levels of H3K27me3 allowed for proper temporal activation of lineage genes during directed differentiation of ESCs to spinal motor neurons (SMNs). However, genes that function to specify other lineages failed to be repressed, suggesting that PRC2 activity is necessary for lineage fidelity. We also found that H3K27me3 is antagonistic to DNA methylation in cis. Furthermore, loss of H3K27me3 leads to a gain in promoter DNA methylation in developmental genes in ESCs and in lineage genes during differentiation. Thus, our data suggest a role for PRC2 in coordinating dynamic gene repression while protecting against inappropriate promoter DNA methylation during differentiation. Embryonic Stem Cell (ESC) lines mutant for PRC2 core components Suz12 (Suz12GT and Suz12delta) and Eed (Eednull) were subjected to in vitro directed differentiation down the spinal motor neuron lineage. ESCs and day 5 differentiated cells from the three mutant lines and wild-type were used for Reduced Representation Bisulfite Sequencing (RRBS).

2014-11-17 | E-GEOD-53507 | biostudies-arrayexpress

PRC2 coordinates lineage fidelity and DNA methylation during ESC differentiation (RNA-Seq)

2014-11-17 | E-GEOD-53506 | biostudies-arrayexpress

PRC2 coordinates lineage fidelity and DNA methylation during ESC differentiation (ChIP-Seq)

2014-11-17 | E-GEOD-53505 | biostudies-arrayexpress

Linker histone H1FOO is required for bovine preimplantation development by regulating lineage specification and nucleosome assembly

Project description:Linker histone H1 binds to the nucleosome and is implicated in the regulation of the chromatin structure and function. The H1 variant H1FOO is heavily expressed in oocytes and early embryos. However, given the poor homology of H1FOO among mammals, the functional role of H1FOO during early embryonic development remains largely unknown, especially in domestic animals. Here, we find that H1FOO is not only expressed in oocytes and early embryos but granulosa cells and spermatids in cattle. We then demonstrate that the interference of H1FOO results in early embryonic developmental arrest in cattle using either RNA editing or Trim-Away approach. H1FOO depletion leads to compromised expression of critical lineage-specific genes at the morula stage and affects the establishment of cell polarity. Interestingly, H1FOO depletion causes a significant increase in expression genes encoding other linker H1 and core histones. Concurrently, there is an increase of H3K9me3 and H3K27me3, two markers of repressive chromatin and a decrease of H4K16ac, a marker of open chromatin. Importantly, overexpression of bovine H1FOO results in severe embryonic developmental defects. In sum, we propose that H1FOO controls the proper chromatin structure that is crucial for the fidelity of cell polarization and lineage specification during bovine early development.

2022-04-11 | GSE197681 | GEO

Variant Polycomb complexes in Drosophila consistent with ancient functional diversity

Project description:Polycomb group (PcG) mutants were first identified in Drosophila based on their failure to maintain proper Hox gene repression during development. The proteins encoded by the corresponding fly genes mainly assemble into one of two discrete Polycomb Repressive Complexes: PRC1 or PRC2. However, biochemical analyses in mammals have revealed alternative forms of PRC2, and multiple distinct types of non-canonical or variant PRC1. Through a series of proteomic analyses, we identify analogous PRC2 and variant PRC1 complexes in Drosophila, as well as a broader repertoire of interactions implicated in early development. Our data provide strong support for the ancient diversity of PcG complexes, and a framework for future analysis in a longstanding and versatile genetic system.

2022-04-29 | GSE201842 | GEO