Control of Embryonic Stem Cell State by Mediator and Cohesin
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Richard Young
PROVIDER: E-GEOD-22557 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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-22562 | biostudies-arrayexpress
Project description:Enhancers are enriched by histone H3 lysine 4 mono methylation (H3K4me1). To gain insight into the relation between enhancers and developmental state, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed in several cell types to determine the genome-wide binding targets of H3K4me1 and several other possible enhancer associated modifications. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A chromatin IP against histone H3 or whole cell extract was sequenced and used as the background to determine enrichment. ChIP was performed mainly using antibodies against the chromatin marks H3K4me1 and H3K27ac.
2010-10-31 | E-GEOD-24164 | biostudies-arrayexpress
Project description:Post-translational modification of histones are coupled to transcription where certain modifications are indicative of an active or inactive region of the genome. Additionally, protein complexes can regulate the placement of nucleosomes across the genome and this influences the ability of DNA-binding proteins to interact with regions of the genome. The datasets presented here are ChIP-seq datasets for chromatin modifications associated with active or poised genes (H2Bub, H3K9,K14Ac and H3K4me3). Brg1 is a subunit of the SWI/SNF chromatin remodeling complex. An antibody specific to the chromatin modification or indicated factor was used to enrich for DNA fragments in murine embryonic stem cells. DNA was purified and prepared for Illumina/Solexa sequencing following their standard protocol.
2012-03-17 | E-GEOD-36561 | biostudies-arrayexpress
Project description:The TATA binding protein (TBP) is a transcription factor that binds specifically to a DNA sequence called the TATA box upstream of the transcription start site. To gain insight into the genes occupied by TBP, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the genome-wide binding targets. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against TBP.
2010-06-15 | E-GEOD-22303 | biostudies-arrayexpress
Project description:Multiple protein complexes and histone marks have been implicated and/or associated with gene repression in ES cells. To gain insights into repressive complexes present at repressed genes and their associated chromatin state, we profiled REST, MCAF1, Ring1b and H4K20me3 in mouse ES cells. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against REST, MCAF1, Ring1b and H4K20me3.
2011-01-19 | E-GEOD-26680 | biostudies-arrayexpress
Project description:Vertebrate condensin I and II molecules are loaded onto the genome to mediate essential changes in chromosome condensation during mitosis, but it is not clear how the two forms of condensin become distributed on chromosomes. We report here that condensin II, the form of condensin present in the nucleus throughout the cell cycle, is loaded at transcriptionally active promoters, migrates through these genes in a transcription-dependent fashion and accumulates in transcription termination regions during interphase. During mitosis, condensin I is recruited to actively transcribed genes and replaces condensin II. We conclude that the two forms of condensin are loaded at different times during the cell division cycle at the promoters of actively transcribed genes. ChIP-Seq data for Condensin II in v6.5 ESCs treated or not with nocodazole
2012-03-14 | E-GEOD-33346 | biostudies-arrayexpress
Project description:Recent studies have found that promoter-proximal pausing occurs at most Pol2-regulated genes. DSIF and NELF function as negative elongation factors and promote Pol2 pausing. P-TEFb, whose enzymatic activity lies in the kinase Cdk9, positively regulates the transition into productive elongation by phosphorylating subunits in DSIF, NELF and Pol2. To gain insights into the interplay between these factors in regulating transcriptional pause release, we tested if knockdown of either pausing factor could bypass P-TEFb function. We find that P-TEFb function is still required for transcriptional elongation after DSIF or NELF knockdown. mES cells were infected with a shRNA hairpin to knockdown Spt5, Spt4, NelfE or control. The resulting cells were then treated with flavopiridol (1uM for 60 minutes). DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total RNA Pol2 (Rpb1 N-terminus, Santa Cruz sc-899).
2011-01-19 | E-GEOD-26658 | biostudies-arrayexpress
Project description:RNA Polymerase II transcribes protein-coding and many non-coding RNA genes in eukaryotes. The largest subunit of RNA Polymerase II, Rpb1, contains a hepta-peptide repeat on its C-terminal tail with three potential phosphorylation sites (Serine 2, Serine 5 and Serine 7). Mammalian Rpb1 contains 52 repeats. The phosphorylation events are catalyzed by specific protein kinases where the phosphorylation of specific residues is coupled to the transcription cycle. For example, the Cdk7 subunit of TFIIH phosphorylates both Serine 5 and Serine 7 during intiation and the Cdk9 subunit of P-TEFb phosphorylates Serine 2 during the transition into productive elongation. The dataset presented here is the genome-wide distribution of RNA Pol II with Serine 7 of the CTD phosphorylated in murine embryonic stem cells. This data, in addition to phospho-specific datasets generated in the same cell type in Rahl et al. Cell 2010 and Seila et al. Science 2008, represents the genome-wide distribution of multiple RNA Pol II isoforms in murine embryonic stem cells: total Pol II, hypophosphorylated CTD Pol II, Serine 2 phosphorylated CTD Pol II, Serine 5 phosphorylated CTD Pol II and Serine 7 phosphorylated CTD Pol II. An antibody specific to RNA Pol II Serine 7 phosphorylated CTD (gift of Dirk Eick; Chapman et al. Science 2008) was used to enrich for DNA fragments associated with this Pol II isoform in murine embryonic stem cells. DNA was purified and prepared for Illumina/Solexa sequencing following their standard protocol. This is a single dataset but together with datasets from Rahl et al. Cell 2010 and Seila et al. Science 2008, these datasets represent the genome-wide distribution of multiple RNA Pol II isoforms in murine embryonic stem cells: total Pol II, hypophosphorylated CTD Pol II, Serine 2 phosphorylated CTD Pol II, Serine 5 phosphorylated CTD Pol II and Serine 7 phosphorylated CTD Pol II.
2010-05-20 | E-GEOD-21917 | biostudies-arrayexpress
Project description:Transcription factors and chromatin modifiers play important roles in programming and reprogramming of cellular states during development. Much is known about the role of these regulators in gene activation, but relatively little is known about the critical process of enhancer silencing during differentiation. Here we show that the H3K4/K9 histone demethylase LSD1 plays an essential role in decommissioning enhancers during differentiation of embryonic stem cells (ESCs). LSD1 occupies enhancers of active genes critical for control of ESC state. However, LSD1 is not essential for maintenance of ESC identity. Instead, ESCs lacking LSD1 activity fail to fully differentiate and ESC-specific enhancers fail to undergo the histone demethylation events associated with differentiation. At enhancers, LSD1 is a component of the NuRD complex, which contains additional subunits that are necessary for ESC differentiation. We propose that the LSD1-NuRD complex decommissions enhancers of the pluripotency program upon differentiation, which is essential for complete shutdown of the ESC gene expression program and the transition to new cell states. This is the ChIP-seq part of the study.
2012-01-03 | E-GEOD-27841 | biostudies-arrayexpress
Project description:Condensin molecules are loaded onto the genome to mediate essential changes in chromosome condensation during mitosis, but it is not clear why there are two forms of vertebrate condensin that become differentially distributed on chromosomes. We report here that condensin II, the form of condensin present in the nucleus throughout the cell cycle, functions specifically at active genes. Condensin II is loaded at transcriptionally active promoters in embryonic stem cells (ESCs), migrates through these genes in a transcription-dependent fashion and accumulates in transcription termination regions. Unlike cohesin, which is also loaded at active promoters, condensin II has little influence on transcription. We conclude that condensin II is loaded and distributed across actively transcribed chromatin and thus serves to specifically condense this euchromatic portion of chromosomes during the cell division cycle. ChIP-Seq data for Condensin II and Cohesin in v6.5 ESCs treated or not with the RNA polymerase II elongation inhibitor flavopiridol.
2012-02-09 | E-GEOD-30919 | biostudies-arrayexpress