Transcriptional control of macrophage inducible gene expression by cohesin [ChIP-Seq II]
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE108805 | GEO | 2018/07/31
REPOSITORIES: GEO
Similar Datasets
Project description:Although cohesin and CTCF are major determinants of interphase 3D genome organisation, their impact on the maintenance of transcriptional control, chromatin marks, and enhancer states appears surprisingly limited. Here we study how cohesin promotes the dynamics of eRNA transcription and enhancer states and facilitates the regulation of inducible inflammatory genes in macrophages.
2018-07-31 | GSE108585 | GEO
Project description:Although cohesin and CTCF are major determinants of interphase 3D genome organisation, their impact on the maintenance of transcriptional control, chromatin marks, and enhancer states appears surprisingly limited. Here we study how cohesin promotes the dynamics of eRNA transcription and enhancer states and facilitates the regulation of inducible inflammatory genes in macrophages.
2018-07-31 | GSE108584 | GEO
Project description:Although cohesin and CTCF are major determinants of interphase 3D genome organisation, their impact on the maintenance of transcriptional control, chromatin marks, and enhancer states appears surprisingly limited. Here we study how cohesin promotes the dynamics of eRNA transcription and enhancer states and facilitates the regulation of inducible inflammatory genes in macrophages.
2018-07-31 | GSE108583 | GEO
Project description:Although cohesin and CTCF are major determinants of interphase 3D genome organisation, their impact on the maintenance of transcriptional control, chromatin marks, and enhancer states appears surprisingly limited. Here we study how cohesin promotes the dynamics of eRNA transcription and enhancer states and facilitates the regulation of inducible inflammatory genes in macrophages.
2018-07-31 | GSE108582 | GEO
Project description:Although cohesin and CTCF are major determinants of interphase 3D genome organisation, their impact on the maintenance of transcriptional control, chromatin marks, and enhancer states appears surprisingly limited. Here we study how cohesin promotes the dynamics of eRNA transcription and enhancer states and facilitates the regulation of inducible inflammatory genes in macrophages.
2018-07-31 | GSE108581 | GEO
Project description:Cohesin is a key regulator of genome architecture with roles in sister chromatid cohesion and the organisation of higher-order structures during interphase and mitosis. The recruitment and mobility of cohesin complexes on DNA are restricted by nucleosomes. Here we show that cohesin role in chromosome organization requires the histone chaperone FACT. Depletion of FACT in metaphase cells affects cohesin stability on chromatin reducing its accumulation at pericentric regions and binding on chromosome arms. Using Hi-C, we show that cohesin-dependent TAD (Topological Associated Domains)-like structures in G1 and metaphase chromosomes are disrupted in the absence of FACT. Surprisingly, sister chromatid cohesion is intact in FACT-depleted cells, although chromosome segregation failure is observed. Our results uncover a role for FACT in genome organisation by facilitating cohesin dependent compartmentalization of chromosomes into loop domains.
2019-10-11 | GSE118534 | GEO
Project description:The organisation of mammalian genomes into loops and topologically associated domains (TADs) regulates gene expression. The formation and maintenance of loops and TADs depends on the protein complex cohesin, which also holds replicated sister chromatids together from S phase until mitosis. To understand how cohesin functions, it is essential to know how many cohesin complexes and regulators exist in a typical cell and how they are distributed genome-wide. Here, we have used quantitative mass spectrometry, fluorescence-correlation spectroscopy and fluorescence recovery after photobleaching to measure the absolute number and dynamics of core subunits and regulators of the cohesin complex in human cells. We find that 60000 – 134000 cohesin complexes are bound to chromatin per G1 HeLa cell, suggesting that cohesin most likely does not occupy all its binding sites concurrently. We incorporate our data into mathematical models and discuss implications for how cohesin might contribute to genome organisation and sister chromatid cohesion.
2019-11-13 | PXD012712 | Pride
Project description:Cohesin is implicated in establishing tissue-specific DNA loops that target enhancers to promoters, and also localizes to sites bound by the insulator protein CTCF, which blocks enhancer-promoter communication. However, cohesin-associated interactions have not been characterized on a genome-wide scale. Here we performed chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) of the cohesin subunit SMC1A in developing mouse limb. We identified 2,264 SMC1A interactions, of which 1,491 (65%) involved sites co-occupied by CTCF. SMC1A participates in tissue- specific enhancer-promoter interactions and interactions that demarcate regions of correlated regulatory output. In contrast to previous studies, we also identified interactions between promoters and distal sites that are maintained in multiple tissues, but are poised in embryonic stem cells and resolve to tissue-specific activated or repressed chromatin states in the mouse embryo. Our results reveal the diversity of cohesin- associated interactions in the genome and highlight their role in establishing the regulatory architecture of development. Smc1a ChIA-PET, RNA-seq, chromatin state maps (H3K27ac, H3K27me3, H3K4m2), and CTCF and Smc1a binding in mouse embryonic limb bud (E11.5)
2013-05-22 | E-GEOD-42237 | biostudies-arrayexpress
Project description:Chromosome conformation capture approaches have shown that interphase chromatin is organized into an architectural framework of Mb-sized compartments and sub-Mb-sized topological domains. Cohesin controls chromosome topology to facilitate DNA repair and chromosome segregation in cycling cells, and also associates with active enhancers and promoters and with CTCF to form long-range interactions important for gene regulation. We find that architectural compartments - a major feature of interphase chromatin organization – are maintained in non-cycling mouse thymocytes after genetic depletion of cohesin in vivo. Cohesin was however required for specific long-range interactions within permissive (A-type) compartments, where cohesin-regulated genes reside. Cohesin depletion diminished interactions between cohesin-bound sites, while alternative interactions between chromatin features associated with transcriptional activation and repression became more prominent, with corresponding changes in gene expression. Our findings indicate that cohesin-mediated long-range interactions facilitate discrete gene expression states within pre-existing chromosomal compartments.
2013-08-13 | GSE48763 | GEO
Project description:Chromatin undergoes major remodeling around DNA double strand breaks (DSB) to promote repair and DNA damage response (DDR) activation. We recently reported a high resolution map of gammaH2AX around multiple breaks on the human genome, using a new cell-based DSB inducible system. In an attempt to further characterize the chromatin landscape induced around DSBs, we now report the profile of SMC3, a subunit from the cohesin complex, previously characterized as required for repair by homologous recombination. We found that the recruitment of cohesin is moderate and restricted to the immediate vicinity of DSBs. In addition, we show that the cohesin complex, which was also recently proposed to be a key player in chromosome organisation and chromatin looping, controls gammaH2AX distribution within domains. Indeed, as we reported for transcription, cohesin binding antagonizes gammaH2AX spreading. Remarkably, depletion of cohesin leads to an increase of gammaH2AX at cohesin-bound genes (revelead by gammaH2AX mapping in upon SCC1 siRNA), associated with a decrease in their expression level after DSB induction. Thus our study identifies a novel role for the cohesin complex in protecting the genes located in gammaH2AX domains from both gammaH2AX spreading and transcriptional shut-down after DSB induction.
2012-01-01 | E-TABM-1164 | biostudies-arrayexpress