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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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The Functional Topography of the Arabidopsis Genome is Defined by Nine Chromatin States that Associate in a Small Number of Motifs

ABSTRACT: Chromatin is of major relevance for gene expression, cell division and differentiation, among other processes. Here we have used 16 chromatin features, including DNA sequence, CG methylation, histone modifications and variants, to obtain a high-resolution landscape of the Arabidopsis chromatin states. The combinatorial complexity of chromatin features can be reduced to 9 states defined by their distinct signatures. These chromatin states preferentially associate with certain genomic elements, gene expression levels, and DNase I accessibility. Each chromatin state has strong propensity to associate with only a subset of other states defining a small number of chromatin motifs. These topographical relationships revealed that Polycomb chromatin physically separates the two heterochromatin states from active chromatin domains. Two paths that mainly differ in their GC content and gene density join active and Polycomb chromatin. The remaining states are associated with active genes: four of them spanning gene bodies and two located upstream of transcription start sites. Our data provide a ground for better understanding the Arabidopsis genome topography and for obtaining new insights into establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains. In total 9 samples; 3 H3K9ac ChIP-chip, 3 H3K14ac ChIP-chip, 3 H3 ChIP-chip

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Xiaoyu Zhang

PROVIDER: E-GEOD-54489 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The Functional Topography of the Arabidopsis Genome is Defined by Nine Chromatin States that Associate in a Small Number of Motifs

Project description:Chromatin is of major relevance for gene expression, cell division and differentiation, among other processes. Here we have used 16 chromatin features, including DNA sequence, CG methylation, histone modifications and variants, to obtain a high-resolution landscape of the Arabidopsis chromatin states. The combinatorial complexity of chromatin features can be reduced to 9 states defined by their distinct signatures. These chromatin states preferentially associate with certain genomic elements, gene expression levels, and DNase I accessibility. Each chromatin state has strong propensity to associate with only a subset of other states defining a small number of chromatin motifs. These topographical relationships revealed that Polycomb chromatin physically separates the two heterochromatin states from active chromatin domains. Two paths that mainly differ in their GC content and gene density join active and Polycomb chromatin. The remaining states are associated with active genes: four of them spanning gene bodies and two located upstream of transcription start sites. Our data provide a ground for better understanding the Arabidopsis genome topography and for obtaining new insights into establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains.

2014-06-01 | GSE54489 | GEO

The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila

Project description:Background: The question of how cells re-establish gene expression states after cell division is still poorly understood. Genetic and molecular analyses have indicated that Trithorax group (TrxG) proteins are critical for the long-term maintenance of active gene expression states in many organisms. A generally accepted model suggests that TrxG proteins contribute to maintenance of transcription by protecting genes from inappropriate Polycomb group (PcG)-mediated silencing, instead of directly promoting transcription. Results: Here we report a physical and functional interaction in Drosophila between two members of the TrxG, the histone methyltransferase ASH1 and the bromodomain and extraterminal family protein FSH. We investigated this interface at the genome level, uncovering a widespread colocalization of both proteins at promoters and PcG-bound intergenic elements. Our integrative analysis of chromatin maps and gene expression profiles revealed that the observed ASH1-FSH binding pattern at promoters is a hallmark of active genes. Inhibition of FSH-binding to chromatin resulted in global down-regulation of transcription. In addition, we found that genes displaying marks of robust PcG-mediated repression also have ASH1 and FSH bound to their promoters. Conclusions: Our data strongly favor a global coactivator function of ASH1 and FSH during transcription, as opposed to the notion that TrxG proteins impede inappropriate PcG-mediated silencing, but are dispensable elsewhere. Instead, our results suggest that PcG repression needs to overcome the transcription-promoting function of ASH1 and FSH in order to silence genes. Refer to individual Series

2013-02-06 | E-GEOD-36450 | biostudies-arrayexpress

Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ES cells (ChIP-Seq)

Project description:Polycomb repressor complexes (PRCs) are important chromatin modifiers fundamentally implicated in pluripotency and cancer. Polycomb silencing in embryonic stem cells (ESCs) can be accompanied by active chromatin and primed RNA polymerase II (RNAPII), but the relationship between PRCs and RNAPII remains unclear at the genome-wide level. We mapped PRC repression markers and four RNAPII states in ESCs using ChIP-seq, and found that PRC-targets exhibit a range of RNAPII variants. Firstly, developmental PRC-targets are bound by unproductive RNAPII (S5p+S7p- S2p-) genome-wide. Sequential ChIP, Ring1B-depletion and genome-wide correlations show that PRCs and RNAPII-S5p physically bind to the same chromatin and functionally synergize. Secondly, we identify a cohort of genes marked by PRC and elongating RNAPII (S5p+S7p+S2p+); they produce mRNA and protein, and their expression increases upon PRC1 knockdown. We show that this novel group of PRC-targets switch between active and PRC-repressed states within the ESC population, and that many have roles in metabolism. **Correction (Mar 14, 2012): Due to curation error, runs for SRX112177 and SRX112179 switched, specifically, Run SRR391034.1 was removed from experiment SRX112177 (GSM850468) and added to experiment SRX112179 (GSM850470) as SRR391034.3 Run SRR391040.1 was removed from experiment SRX112179 (GSM850470) and added to experiment SRX112177 (GSM850468) as SRR391040.3 Examination of 4 different RNAPII modifications (S5p, S7p, 8WG16, S2p), and the histone modifications H2Aub1 and H3K36me3 in mouse ES cells

2012-02-01 | E-GEOD-34518 | biostudies-arrayexpress

Histone acetylation H2BK20ac marks cell-state specific active regulatory elements

Project description:Characterisation of different histone modifications is crucial to understand gene regulation. In order to study the most predictive histone modification for active enhancers we created unbiased set of enhancers and used machine learning approach. Our approach revealed an unconventional histone modification H2BK20ac as most efficient marker of active enhancers. H2BK20ac also showed superior coverage of tissue specific active enhancers in complex invivo samples. Adding H2BK20ac to set of conventional histone modifications lead to identification of new chromatin state which could be active enhancers. H2BK20ac tends to occur only at cell-type specific active promoters and showed higher specificity for related disease mutations than H3K27ac and other histone modifications. Using transient state of BV2 microglia cells after lipopolysaccharide based activation, we found that H2BK20ac also marks cell-state specific cis-regulatory elements. Further analysis using inhibition of TGF-beta pathway in BV2 cells and LPS stimulation, revealed differential patterns of H2BK20ac and H3K27ac at genome locations associated with opposite roles response to stmulation. Our study about H2BK20ac hints about a new mechanism of regulation of cell-type specificity and a distinct mode of action of pathways to maintain balance between cell-responses. Chip-seq of H2BK20ac and other histone modifcation was performed in 3 cell types and embryonic mouse forebrain. The sensitivity for active enhancers was compared for different histone modification ChIP-seq.The level of H2BK20ac at promoters and enhancers was assesed for relationship to cell-type specific expression. H2BK20ac signals were also analysed during cell-state transition when microgila are stimulated by LPS

2016-02-25 | E-GEOD-72886 | biostudies-arrayexpress

ChIP-MS reveals the local chromatin composition by label-free quantitative proteomics

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2023-12-10 | PXD042826 | Pride

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

Project description:The histone variant H2A.Z has been implicated in nucleosome exchange, transcriptional activation and Polycomb repression. However, the relationships among these seemingly disparate functions remain obscure. We mapped H2A.Z genome-wide in mammalian ES cells and neural progenitors. H2A.Z is deposited promiscuously at promoters and enhancers, and correlates strongly with H3K4 methylation. Accordingly, H2A.Z is present at poised promoters with bivalent chromatin and at active promoters with H3K4 methylation, but is absent from stably repressed promoters that are specifically enriched for H3K27 trimethylation. We also characterized post-translational modification states of H2A.Z, including a novel species dually-modified by ubiquitination and acetylation that is enriched at bivalent chromatin. Our findings associate H2A.Z with functionally distinct genomic elements, and suggest that post-translational modifications may reconcile its contrasting locations and roles. Examination of histone variant, histone modifications and transcription machinery in 3 cell types

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Bivalency - Histone H3 Lysine4 and Histone H3 Lysine27 Methylation Dynamics

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