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Genomic and proteomic resolution of heterochromatin and its restriction of alternate fate genes (ChIP-seq)

ABSTRACT: Heterochromatic regions in mammalian cells suppress recombination, silence transcription, and are crucial for maintaining cell differentiation. Genomic and biochemical characterization of heterochromatin has relied on the associated histone modifications H3K9me3 and H3K27me3, yet these marks are also found in euchromatic regions that permit transcription. We employed a biophysical method to isolate sonication resistant heterochromatin from human somatic cells, mapped its genomic organization compared to histone modifications, and used proteomics to reveal an extensive number of heterochromatin-bound proteins. We discriminate subtypes of H3K9me3- and H3K27me3-marked domains, in sonication-resistant heterochromatin versus euchromatin, and we present a resource of hundreds of proteins that preferentially bind heterochromatin, a set enriched for RNA-binding proteins and proteins that oppose iPS reprogramming. The sonication-resistant heterochromatin landscape includes repressed genes for alternative lineages that are resistant to activation by introduced transcription factors. Depletion of identified heterochromatin-associated proteins reduces this barrier, rendering alternative-lineage genes more competent for transcriptional activation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE87039 | GEO | 2017/12/21

SECONDARY ACCESSION(S): PRJNA343266

REPOSITORIES: GEO

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Genomic and proteomic resolution of heterochromatin and its restriction of alternate fate genes (RNA-seq)

Project description:Heterochromatic regions in mammalian cells suppress recombination, silence transcription, and are crucial for maintaining cell differentiation. Genomic and biochemical characterization of heterochromatin has relied on the associated histone modifications H3K9me3 and H3K27me3, yet these marks are also found in euchromatic regions that permit transcription. We employed a biophysical method to isolate sonication resistant heterochromatin from human somatic cells, mapped its genomic organization compared to histone modifications, and used proteomics to reveal an extensive number of heterochromatin-bound proteins. We discriminate subtypes of H3K9me3- and H3K27me3-marked domains, in sonication-resistant heterochromatin versus euchromatin, and we present a resource of hundreds of proteins that preferentially bind heterochromatin, a set enriched for RNA-binding proteins and proteins that oppose iPS reprogramming. The sonication-resistant heterochromatin landscape includes repressed genes for alternative lineages that are resistant to activation by introduced transcription factors. Depletion of identified heterochromatin-associated proteins reduces this barrier, rendering alternative-lineage genes more competent for transcriptional activation.

2017-12-21 | GSE87040 | GEO

Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (ChIP-seq)

Project description:Heterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partially overcome by inducing ectopic transcription factors (TFs) to activate an alternative transcriptional program. However, TFs are impeded by highly restrictive heterochromatin leading to low reprogramming rates and incomplete activation of the target transcriptome. Previously we utilized the heterochromatin property of sonication resistance to identify 172 proteins associated with sonication resistant heterochromatin (srHC) by mass spectrometry (Becker, et al., 2017). We hypothesized that by functionally assessing the srHC proteins and identifying the genes they repress during reprogramming we could improve our understanding of heterochromatin maintenance and learn how to disrupt heterochromatin to enhance reprogramming. Focusing on reprogramming from fibroblasts to induced human hepatocytes (hiHeps) we conducted an siRNA screen of 97 srHC proteins without reprogramming factors (noTF) and with hiHep reprogramming and assessed the impact on the expression of genes located in srHC domains by RNA-seq. We identified enhancer of rudimentary homolog (ERH) as a key regulator of H3K9me3 heterochromatin maintenance. ERH was found to associate broadly with H3K9me3 domains and when depleted caused global changes in H3K9me3 and srHC. Collectively our screen of srHC protein repressive function demonstrates specific functionality of groups of srHC proteins and increases our understanding of H3K9me3 gene repression.

2021-06-24 | GSE154214 | GEO

Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (RNA-seq)

2021-06-24 | GSE154148 | GEO

Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (srHC-seq)

2021-06-24 | GSE154232 | GEO

ChIP-seq of histone marks of DP thymocytes from Suv39h1 and Suv39h2 double knockout chimeric mice

Project description:H3K9me3-dependent heterochromatin is critical for the silencing of repeat-rich pericentromeric regions and also has key roles in repressing lineage-inappropriate protein-coding genes for healthy cellular function. Within all eukaryotic nuclei, heterochromatin and euchromatin are spatially segregated, with euchromatin typically located in the nuclear interior and heterochromatin at the nuclear periphery. Here we investigate the histone modifications (H3K27ac, H3K27me3, H3K4me3 and H3K9me3) in the absence of H3K9me3-dependent heterochromatin by performing ChIP-seq in primary immune cells deficient in both Suv39h1 and Suv39h2 (Suv39DKO), the major mammalian histone methyltransferase enzymes which catalyse heterochromatic H3K9me3 deposition.

2024-03-27 | GSE256245 | GEO

Discrete genomic domains exhibit co-occurrence of H3K9me3 and H3K27me3 histone modifications throughout Drosophila

Project description:Full title: Discrete genomic domains exhibit co-occurrence of H3K9me3 and H3K27me3 histone modifications throughout Drosophila development Trimethylation of histone H3 on lysine 9 (H3K9me3) and lysine 27 (H3K27me3) is strongly associated with gene silencing and transcriptional repression in both Drosophila and mammals. H3K9me3 is linked to the formation of heterochromatin, while H3K27me3 is a hallmark of repression of euchromatic genes by Polycomb group proteins. We examined the genomic distribution of the two modifications at high resolution over nine different stages of Drosophila development, and found that they are present in large overlapping domains in euchromatin. These dual-mark domains are stable throughout the life of the fly, and cover genomic regions greatly enriched in developmental regulatory genes with spatially restricted expression. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

2009-10-16 | GSE18572 | GEO

Chromatin immunoprecipitation of Arabidopsis seedlings to identify targets of TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1 and H3K27me3, H3K9me2 and H3K9me3

Project description:Chromatin immunoprecipitation and hybridization to a chromosome-wide DNA tiling array (ChIP-chip)was performed to identify the targets of the chromatin protein TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1. Epigenomic profiling was also carried out for three histone H3 modifications: H3K27me3, H3K9me2 and H3K9me3. Experiments were done using two independent biological replicates.

2007-04-17 | E-MEXP-951 | biostudies-arrayexpress

Examining the effect of the linker DNA length on protein binding to di-nucleosomes decorated with H3K9me3 and H3K27me3

Project description:Characteristic features of chromatin states are not limited to particular epigenetic modifications but include other regulatory cues, such as linker DNA length, typically ranging from between 35-55 bp (Valouev et al, 2011; Voong et al., 2016, Cell) to over 200 bp in nucleosome-depleted regions (NDRs) found at active enhancers and promoters (Schones et al, 2008; Hansen He et al, 2010). To investigate whether and how the nucleosome linker DNA affects chromatin recognition by nuclear proteins we performed a set of affinity purifications using di-nucleosomes incorporating different DNA linkers. This dataset contains experiments aimed to probe how the linker DNA length affects protein binding to di-nucleosomes decorated with H3K9me3 or H3K27me3. The following di-nucleosomes were used in affinity pull-down purifications with HeLa nuclear extract followed by label-free MS: 1. unmod. H3, 35 bp linker 2. unmod. H3, 40 bp linker 3. unmod. H3, 45 bp linker 4. unmod. H3, 50 bp linker 5. unmod. H3, 55 bp linker 6. H3K9me3, 35 bp linker 7. H3K9me3, 40 bp linker 8. H3K9me3, 45 bp linker 9. H3K9me3 50 bp linker 10. H3K9me3, 55 bp linker 11. H3K27me3, 35 bp linker 12. H3K27me3, 40 bp linker 13. H3K27me3, 45 bp linker 14. H3K27me3, 50 bp linker 15. H3K27me3, 55 bp linker

2023-12-10 | PXD042368 | Pride

Gene Expression and Histone Modification Profiles in GBM Tumors

Project description:<p>The primary goal of this study was to collect and analyze genomic data from primary glioblastoma multiforme tumors. Our collaborators at St David's Medical Center (SDMC) obtained informed consent from patients undergoing surgery to remove a tumor in the brain. After consent was obtained, specimens were removed from the operating suite and flash frozen in liquid nitrogen. Tumors were analyzed if they were a grade III (anaplastic astrocytoma) or grade IV glioma (glioblastoma multiforme). Tumors were transported from SDMC to UT Austin, then weighed and homogenized. Chromatin immunoprecipitation was performed for 7 proteins in each tumor (histone modifications H3K4me3, H3K4me1, H3K9ac, H3K9me3, H3K27ac, H3K27me3, and the multifunctional insulator binding protein CTCF) and no-antibody input was also sequenced. An aliquot of tumor material was set aside for isolation of total RNA.</p>

| phs001389 | dbGaP

Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa

Project description:Both RNAi-dependent and -independent mechanisms have been implicated in the establishment of heterochromatin domains, which may be stabilized by feedback loops involving chromatin proteins and modifications of histones and DNA. Neurospora crassa sports features of heterochromatin found in higher eukaryotes, namely cytosine methylation (5mC), methylation of histone H3 lysine9 (H3K9me) and HETEROCHROMATIN PROTEIN-1 (HP1), and provides a model to investigate heterochromatin establishment and maintenance. We mapped the distribution of HP1, 5mC, H3K9me3 and H3K4me2 at 100bp-resolution and explored their interplay. HP1, H3K9me3 and DNA methylation were extensively colocalized and defined 44 heterochromatic domains on linkage group VII, all relics of repeat-induced point mutation (RIP). Interestingly, the centromere was found in a striking ~350kb heterochromatic domain with no detectable H3K4me2. 5mC was not found in genes, in contrast to the situation in plants and animals. H3K9me3 is required for HP1 localization and DNA methylation. Here, we show that localization of H3K9me3 is independent of 5mC or HP1 at virtually all heterochromatin regions. In addition, we observed complete restoration of DNA methylation patterns after depletion and reintroduction of the H3K9 methylation machinery, indicating that the signals for de novo heterochromatin formation lie upstream of H3K9 methylation. These data show that A:T rich RIPâd DNA efficently directs methylation of H3K9, which in turn, directs methylation of associated cytosines. Immunoprecipitation experiments using antibodies to 5mC, H3K9me3, epitope-tagged HP1, and H3K4me2 were performed. The immunoprecipitate fraction was labeled with Cy5 and the total input was labeled with Cy3. Samples were hybridized to a N. crassa LGVII tiling path microarray.

2010-05-15 | E-GEOD-12690 | biostudies-arrayexpress

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