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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Specificity, propagation and memory of pericentric heterochromatin in mouse fibroblasts

ABSTRACT: We assembled a quantitative map for the abundance and interactions of 16 factors related to PCH in living cells and found that stably bound complexes of the histone methyltransferase Suv39h1/2 demarcate the PCH state. From the experimental data we developed a predictive mathematical model that explains how chromatin-bound Suv39h1/2 complexes act as nucleation sites and propagate a spatially confined PCH domain with elevated histone H3 trimethylation levels via chromatin dynamics. Enrichment of HP1, Suv39h1/h2, H3K9me3 and H3K36me3 was assessed by ChIP-seq in NPCs derived from ESCs showing differential occupation at intergenic major satellite repeats and enrichment of heterochromatin factors. ChIP-seq of HP1, Suv39h1, Suv39h2, H3K9me3, H3K36me3 in NPCs

ORGANISM(S): Mus musculus

SUBMITTER: Jan-Philipp Mallm

PROVIDER: E-GEOD-58555 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Specificity, propagation, and memory of pericentric heterochromatin.

Müller-Ott Katharina K Erdel Fabian F Matveeva Anna A Mallm Jan-Philipp JP Rademacher Anne A Hahn Matthias M Bauer Caroline C Zhang Qin Q Kaltofen Sabine S Schotta Gunnar G Höfer Thomas T Rippe Karsten K

Molecular systems biology 20140818

The cell establishes heritable patterns of active and silenced chromatin via interacting factors that set, remove, and read epigenetic marks. To understand how the underlying networks operate, we have dissected transcriptional silencing in pericentric heterochromatin (PCH) of mouse fibroblasts. We assembled a quantitative map for the abundance and interactions of 16 factors related to PCH in living cells and found that stably bound complexes of the histone methyltransferase SUV39H1/2 demarcate t ...[more]

PMID: 25134515

Similar Datasets

Specificity, propagation and memory of pericentric heterochromatin in mouse fibroblasts

Project description:We assembled a quantitative map for the abundance and interactions of 16 factors related to PCH in living cells and found that stably bound complexes of the histone methyltransferase Suv39h1/2 demarcate the PCH state. From the experimental data we developed a predictive mathematical model that explains how chromatin-bound Suv39h1/2 complexes act as nucleation sites and propagate a spatially confined PCH domain with elevated histone H3 trimethylation levels via chromatin dynamics. Enrichment of HP1, Suv39h1/h2, H3K9me3 and H3K36me3 was assessed by ChIP-seq in NPCs derived from ESCs showing differential occupation at intergenic major satellite repeats and enrichment of heterochromatin factors.

2014-08-12 | GSE58555 | GEO

Loss of H3K9 tri-methylation alters chromosome compaction and transcription factor retention during mitosis

Project description:Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases and Polycomb Repressor Complexes, bind to chromosomes throughout mitosis and their depletion results in increased chromosome size. Here we show that enzymes that catalyse H3K9 methylation, such as Suv39h1, Suv39h2, G9a and Glp, are also retained on mitotic chromosomes. Surprisingly however, mutants lacking H3K9me3 have unusually small and compact mitotic chromosomes associated with increased H3S10ph and H3K27me3 levels. Chromosome size and centromere compaction in these mutants were rescued by providing exogenous Suv39h1, or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wildtype versus Suv39h1/Suv39h2 double-null mouse ESCs revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis, and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.

2023-01-25 | PXD039521 | Pride

Loss of H3K9 tri-methylation alters mitotic chromosome compaction and transcription factor retention during mitosis

Project description:Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases (DNMTs) and Polycomb Repressor Complexes (PRCs), bind to chromosomes throughout mitosis and their depletion results in increased chromosome size. Enzymes that catalyse H3K9 methylation, such as Suv39h1, Suv39h2, G9a, GLP are also retained by mitotic chromosomes. Surprisingly however, mutants lacking H3K9me3 have unusually small and compact mitotic chromosomes that are associated with increased H3S10ph and H3K27me3 levels. Chromosome size and centromere compaction in these mutants was rescued by providing exogenous Suv39h1, or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wildtype versus Suv39h1,2 double null ESCs revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis, and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.

2022-10-12 | PXD030771 | Pride

proj022_chipseq

Project description:The mechanisms that recruit the major Polycomb-group (PcG) complexes PRC1 and PRC2 to target sites in vertebrate cells are not well understood. Building on recent studies that have determined a reciprocal relationship between DNA methylation and Polycomb activity, we demonstrate that in methylation deficient ES cells CpG density, combined with antagonistic effects of H3K9me3 and H3K36me3, redirect PcG complexes to pericentric heterochromatin and gene rich domains. In this experiment we have assayed the genomic distribution of H3K9me3 and H3K36me3 marks,

2014-05-23 | E-MTAB-2481 | biostudies-arrayexpress

Reader interactome of epigenetic histone marks in birds

Project description:Lysine methylation is part of the posttranscriptional histone code employed to recruit modification specific readers to chromatin. Unbiased, quantitative mass spectrometry approaches combined with peptide pull-downs have been used to study histone methylation-dependent binders in mammalian cells. Here, we extend the study to birds by investigating the interaction partners for H3K4me3, H3K9me3, H3K27me3 and H3K36me3 in chicken (gallus gallus) and zebra finch (taeniopygia guttata) using label free quantitative proteomics. In general, we find very strong overlap in interaction partners for the trimethyl marks in birds compared to mammals, underscoring the known conserved function of these modifications. In agreement with their epigenetic role, we find binding of PHF2 and members of the TFIID, SAGA, SET1 and NURF complex to the activation mark H3K4me3. Our data furthermore supports the existence of a LID complex in vertebrates recruited to the H3K4me3. The repressive marks are bound by the HP1 proteins and the EED subunit of the PRC2 complex as well as by WIZ. Like the screens in mammals, we found ZNF462, ZNF828 and POGZ enriched at H3K9me3. However, we noted some unexpected differences. First, we did not observe the enrichment of CDYL and CDYL2 at the repressive marks. Second N-PAC (also known as GLYR1), an H3K36me3 interactor in mammals, is not binding to this modification in our screen. This suggests that despite strong conservation of the histone tail sequence, species-specific differences in epigenetic readers may have evolved.

2016-01-04 | PXD002282 | Pride

Loss of histone demethylase JARID1C triggers genomic instability in cancer.

Project description:Chromatin remodelers are recurrently mutated in cancer. Among these, JARID1C, (KDM5C) a histone demethylase, is frequently inactivated in clear cell renal cell carcinoma (ccRCC) patients. How the genetic inactivation of JARID1C leads to cancer remains largely unknown. Here we report that JARID1C binds to broad chromatin domains characterized by the trimethylation of lysine 9 (H3K9me3), an histone mark enriched in heterochromatin. We also found that JARID1C localizes on heterochromatin, is required for heterochromatin replication, and forms a complex with established and novel players of heterochromatin assembly, such as SUV39H1 and HP1 and the CUL4 complex adaptor protein DDB1, respectively. To safeguard the genome, transcription on heterochromatin is tightly suppressed. JARID1C inactivation leads to the unrestrained expression of heterochromatic ncRNAs, that in turn trigger genomic instability. Remarkably, ccRCC patients harbouring JARID1C mutations show aberrant ncRNA expression and increased genomic rearrangements when compared with tumors endowed with other genetic lesions. Together, these data suggest that the inactivation of JARID1C in renal cancer leads to heterochromatin disruption and to aggressive, genomically rearranged ccRCCs, shedding light on a novel mechanism underlying genomic instability in sporadic cancers. We performed ChIP-sequencing for KDM5C, H3K9me3, H3K4me1 and H3K4me3 in Caki-1 untreated cells. Platform HiSeq2500.

2015-11-09 | E-GEOD-73267 | biostudies-arrayexpress

Loss of H3K9 tri-methylation alters mitotic chromosome compaction and transcription factor retention during mitosis

Project description:Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases (DNMTs) and Polycomb Repressor Complexes (PRCs), bind to chromosomes throughout mitosis and their depletion results in increased chromosome size. Enzymes that catalyse H3K9 methylation, such as Suv39h1, Suv39h2, G9a, GLP are also retained by mitotic chromosomes. Surprisingly however, mutants lacking H3K9me3 have unusually small and compact mitotic chromosomes that are associated with increased H3S10ph and H3K27me3 levels. Despite these differences, chromatin accessibility, as measured by ATAC-seq, was broadly similar between genotypes. Chromosome size and centromere compaction in these mutants was rescued by providing exogenous Suv39h1, or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wildtype versus Suv39h1,2 double null ESCs revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis, and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.

2023-01-17 | GSE195767 | GEO

ChIP-Seq of FBXO44 and H3K9me3 in MDA-MB-231

Project description:FBXO44 bound H3K9me3-modified nucleosomes at the replication fork and recruited the H3K9me3 methyltransferase SUV39H1 for repetitive element silencing post-DNA replication

2021-03-26 | GSE139973 | GEO

Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription

Project description:This SuperSeries is composed of the following subset Series: GSE26018: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuEx-1_0-st] GSE26019: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuGene-1_0-st] GSE26038: Crosstalk between gene body DNA methylation, H3K9me3 and H3K36me3 chromatin marks and transcription [HuEx-1_0-st, transcript] GSE26040: Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks Refer to individual Series

2011-03-31 | E-GEOD-26020 | biostudies-arrayexpress

H3K9me3 ChIP-seq analysis of in vitro cultured littermate and Suv39h1-KO CD8+ T cells

Project description:H3K9me3 mark deposition by the histone methyltransferase Suv39h1 during CD8+-T cell differentiation in vitro

2018-01-17 | GSE106265 | GEO