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Control of Embryonic Stem Cell State by Mediator and Cohesin (Illumina ChIP-Seq data)

ABSTRACT: The key transcription factors that control the embryonic stem cell gene expression program have been identified, but how they function to implement this program is not well understood. While screening for genes essential for maintenance of ES cell state, we identified many components of the Mediator and Cohesin complexes. Mediator and Cohesin were found to physically and functionally connect the enhancers and core promoters of active genes. An ES cell Mediator complex was found to copurify with Cohesin and its loading factor Nipbl, and normal levels of these proteins were essential for expression of the genes they occupy and for maintenance of ES cell state.

ORGANISM(S): Mus musculus

PROVIDER: GSE22562 | GEO | 2010/08/12

SECONDARY ACCESSION(S): PRJNA129097

REPOSITORIES: GEO

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Control of Embryonic Stem Cell State by Mediator and Cohesin (Agilent gene expression data)

Project description:The key transcription factors that control the embryonic stem cell gene expression program have been identified, but how they function to implement this program is not well understood. While screening for genes essential for maintenance of ES cell state, we identified many components of the Mediator and Cohesin complexes. Mediator and Cohesin were found to physically and functionally connect the enhancers and core promoters of active genes. An ES cell Mediator complex was found to copurify with Cohesin and its loading factor Nipbl, and normal levels of these proteins were essential for expression of the genes they occupy and for maintenance of ES cell state. See associated publication.

2010-08-12 | E-GEOD-22556 | biostudies-arrayexpress

Control of Embryonic Stem Cell State by Mediator and Cohesin (Illumina ChIP-Seq data)

2010-08-12 | E-GEOD-22562 | biostudies-arrayexpress

Control of Embryonic Stem Cell State by Mediator and Cohesin (Agilent gene expression data)

2010-08-12 | GSE22556 | GEO

FOXA and master transcription factors recruit Mediator and Cohesin to the core transcriptional regulatory circuitry of cancer cells

Project description:The Mediator and Cohesin complexes control the cellular transcriptional program. However, it is not well understood how they are recruited to regulatory regions. Our study shows that the core transcriptional regulatory circuitry of cancer cells is essential to recruit Mediator, Cohesin and NIPBL to enhancer and promoter regions of actively transcribed genes in cancer cells. ChIP-seq analysis of Mediator (MED1), Cohesin (SMC1A) and NIPBL in HEPG2, A549 and MCF7 cells. The analysis also includes ChIP-Seq data for the transcription factor ERa in MCF7 cells treated with estradiol.

2016-10-24 | E-GEOD-76893 | biostudies-arrayexpress

ChIP-Seq for NIPBL for SMC1 in human lymphoblastoid cells (hLCLs)

Project description:The gene expression program is regulated by a cell-type specific chromosome architecture. The connection between enhancer and promoter regions is dependent on a protein complex containing Nipbl, Mediator and Cohesin. To gain insights into the chromosome architecture of human differentiated cells, we profiled NIPBL and SMC1 in lymphoblastoid cells (LCLs). DNA was enriched from hLCLs and chromatin immunoprecipitations (ChIPs) were analyzed by Solexa sequencing. ChIPs were performed using an antibody against NIPBL and SMC1. Whole cell extract is provided for background.

2012-06-01 | E-GEOD-38395 | biostudies-arrayexpress

ChIP-Seq for NIPBL for SMC1 in human lymphoblastoid cells (hLCLs)

2012-06-01 | GSE38395 | GEO

FOXA and master transcription factors recruit Mediator and Cohesin to the core transcriptional regulatory circuitry of cancer cells

2016-10-24 | GSE76893 | GEO

Gene expression changes in limb buds of Nipbl-haploinsufficient mice

Project description:Multiple genes are dysregulated in hindlimb buds of Nipbl-deficient embryos. In all, more than 1000 limb bud genes were found to be significantly altered in expression by microarray analysis of E10.5 mouse hindlimb buds. Small changes in expression (mostly decreases) were observed for genes involved in FGF, BMP, and SHH pathways, as well as numerous genes involved in the Wnt/planar cell polarity signaling pathway. Genes involved in the Mediator complex, Cohesin function, and Hox gene expression and functions were also dysregulated in Nipbl deficient limb buds. Microarray analysis using RNA extracted from E10.5 hindlimb limb buds harvested from stage-matched Nipbl+/- (n=12) and wildtype (n=12)

2014-08-30 | E-GEOD-60932 | biostudies-arrayexpress

Control of Embryonic Stem Cell State by Mediator and Cohesin

Project description:This SuperSeries is composed of the following subset Series: GSE22556: Control of Embryonic Stem Cell State by Mediator and Cohesin (Agilent gene expression data) GSE22562: Control of Embryonic Stem Cell State by Mediator and Cohesin (Illumina ChIP-Seq data) Refer to individual Series

2010-08-11 | E-GEOD-22557 | biostudies-arrayexpress

ChIP Seq Analysis of SCC2 in the Presence or Absence of MED14 in Saccharomyces cerevisiae

Project description:The ring-like cohesin complex plays an essential role in chromosome segregation, organization, and double-strand break repair through its ability to bring two DNA double helices together. Scc2 (NIPBL in humans) together with Scc4 function as the loader of cohesin onto chromosomes. Chromatin adapters such as the RSC complex facilitate localization of the Scc2-Scc4 cohesin loader. Here we identify a broad range of Scc2- chromatin protein interactions that are evolutionarily conserved and reveal a role for one complex, Mediator, in recruitment of the cohesin loader. We identified budding yeast Med14, a subunit of the Mediator complex, as a high copy suppressor of poor growth in Scc2 mutant strains. Physical and genetic interactions between Scc2 and Mediator are functionally substantiated in direct recruitment and cohesion assays. Depletion of Med14 results in defective sister chromatid cohesion and decreased binding of Scc2 at RNA Pol II transcribed genes. Previous work has suggested that Mediator, Nipbl, and cohesin connect enhancers and promoters of active mammalian genes. Our studies suggest an evolutionarily conserved fundamental role for Mediator in direct recruitment of Scc2 to RNA pol II transcribed genes. We identified two mutations in the evolutionarily conserved HEAT domain of SCC2 that result in significantly reduced growth, scc2R787G and scc2G1242V. This experiment uses ChIP Seq to examine global localization of Scc2 in the presence or absence of MED14.

2022-05-25 | GSE201193 | GEO

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