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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MRNA-seq and expression profile of mouse ES OS25 cells

ABSTRACT: mRNA-seq and expression profile of mouse ES OS25 cells Gene expression (mRNA-Seq) in mouse ES cells

ORGANISM(S): Mus musculus

SUBMITTER: Ines Santiago

PROVIDER: E-GEOD-34519 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs.

Brookes Emily E de Santiago Inês I Hebenstreit Daniel D Morris Kelly J KJ Carroll Tom T Xie Sheila Q SQ Stock Julie K JK Heidemann Martin M Eick Dirk D Nozaki Naohito N Kimura Hiroshi H Ragoussis Jiannis J Teichmann Sarah A SA Pombo Ana A

Cell stem cell 20120201 2

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 genome-wide. 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. First, developmental PRC targets ...[more]

PMID: 22305566

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

Project description:This SuperSeries is composed of the following subset Series: GSE34518: Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ES cells (ChIP-Seq) GSE34519: mRNA-seq and expression profile of mouse ES OS25 cells Refer to individual Series

2012-02-01 | E-GEOD-34520 | 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

Expanding the CTD code: methylation of non-consensus Lysine residues marks early transcription in mammalian cells

Project description:Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and co-transcriptional processing of nascent RNA. Extensive phosphorylation of serine residues occurs at the structurally-disordered C-terminal domain (CTD) of the largest RNAPII subunit, which is composed of multiple heptapeptide repeats with consensus sequence Y1-S2-P3-T4-S5-P6-S7. Serine-5 and Serine-7 phosphorylation mark transcription initiation, whereas Serine-2 phosphorylation coincides with productive elongation. In vertebrates, the CTD has eight non-canonical substitutions of Serine-7 into Lysine-7, which can be acetylated (K7ac). Here, we describe for the first time mono- and di-methylation of CTD Lysine-7 residues (K7me1 and K7me2). K7me1 and K7me2 are observed during the earliest transcription stages and precede or accompany Serine-5 and Serine-7 phosphorylation. Genome wide mapping of 2 novel RNAPII post-translational modifications (CTD-K7me1 and CTD-K7me2) in mouse ES cells.

2015-12-22 | E-GEOD-72876 | biostudies-arrayexpress

Transposable elements and their KRAB-ZFP controllers regulate gene expression in adult tissues

Project description:The tetrapod-restricted KRAB-containing zinc finger proteins (KRAB-ZFPs) are essential early embryonic controllers of transposable elements (TEs), which they repress via their cofactor KAP1 and associated effectors through histone and DNA methylation, a process thought to result in irreversible silencing. Using a target-centered functional screen, we matched several murine TEs with their cognate KRAB-ZFP. This revealed an unexpected level of granularity in their interactions, with KRAB-ZFPs recognizing TEs from more than one subfamily, TEs recruiting more than one KRAB-ZFP, and spatially and temporally differential KRAB-ZFP-mediated regulation of TEs and nearby genes. Most importantly, we discovered that the KRAB/KAP1 system controls TEs in adult tissues, in cell culture and in vivo, where they partner up to regulate the expression of cellular genes. Therefore, TEs and KRAB-ZFPs establish widely active transcription networks that regulate not only development but probably also many physiological events. Given the high degree of species-specificity of both TEs and KRAB-ZFPs, these results have important implications for studying and understanding the biology of higher vertebrates, including humans. Analysis of transcriptional profiles of KAP1 or ZFP932/Gm15446 KO cells or tissues, and ZFP932 and Gm15446 ChIPseq in murine ES and C2C12 cells.

2016-03-15 | E-GEOD-74278 | biostudies-arrayexpress

Murine Embryonic Stems Cells: H3K27me3 in Undifferentiated (UD) and Day 3 (D3) differentiated ES cells

Project description:ChIP on chip for H3K27me3 in murine ES cells comparing Undifferentiated and Day 3 differentiated. Paper Abstract: How polycomb group proteins repress gene expression in vivo is not known. Whilst histone modifying activities of the polycomb repressive complexes have been studied extensively, in vitro data has suggested a direct activity of the PRC1 complex in compacting chromatin. Here, we investigate higher-order chromatin compaction of polycomb targets in vivo. We show that polycomb repressive complexes are required to maintain a compact chromatin state at Hox loci in embryonic stem (ES) cells. There is specific decompaction in the absence of PRC2 or PRC1. This is due to PRC1, since decompaction occurs in Ring1B null cells that still have PRC2-mediated H3K27 methylation. Moreover, we show that the ability of Ring1B to restore a compact chromatin state, and to repress Hox gene expression in ES cells, is not dependent on its histone ubiquitination activity. We suggest that Ring1B-mediated chromatin compaction acts to directly limit transcription in vivo. Biological replicates: 3 independently grown, harvested, micrococcal nuclease digested and ChIP for H3K27me3. 6 Technical replicates.

2010-05-14 | E-GEOD-20201 | biostudies-arrayexpress

TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells

Project description:TRIM28 (KAP1 - KRAB-associated protein 1) is critical for the silencing of endogenous retroviruses (ERVs) in embryonic stem (ES) cells. Here, we reveal that an essential impact of this process is the protection of cellular gene expression in early embryos from perturbation by cis-acting activators contained within these genetic invaders. In TRIM28-depleted ES cells, repressive chromatin marks at ERVs are replaced by histone modifications typical of active enhancers, stimulating transcription of nearby cellular genes, notably those harboring bivalent promoters. Correspondingly, ERV-derived sequences can repress or enhance expression from an adjacent promoter in transgenic embryos depending on their TRIM28-sensitivity in ES cells. TRIM28-mediated control of ERVs is therefore crucial not just to prevent retrotransposition, but more broadly to safeguard the transcriptional dynamics of early embryos. Analyses of transcriptional profiles and chromatin state in TRIM28 WT and KO cells

2012-12-04 | E-GEOD-41903 | biostudies-arrayexpress

2C::tomato ES cells, 2-cell embryos and wild type oocytes

Project description:This SuperSeries is composed of the following subset Series: GSE33763: Expression data from 2C::tomato+ vs 2C::tomato - ES cells GSE33920: mRNA-Seq of 2C::tomato+ vs. - ES cells GSE33921: RNA-Seq from two-cell (2C) stage embryos GSE33922: RNA-Seq from wt oocytes GSE36896: RNA-Seq from wt and G9A knockout ES cells Refer to individual Series

2012-06-17 | E-GEOD-33923 | biostudies-arrayexpress

Epigenome and transcriptome of naive pluripotent mouse embryonic stem (ES) cells cultured in 2i serum-free medium

Project description:This study describes the epigenetic and transcriptome profiling of mouse ES cells cultures in 2i serum-free medium. The proteins for which ChIP-Seq profiles were generated in these cells, as well as for cells grown in serum conditions, include H3K4me3, H3K36me3, H3K27me3, H3K9me3, Suz12 and Ezh2. A sequence profile of genomic DNA is also included. Furthermore, we included RNA-Seq of ds_cDNA synthesized from double poly(A) selected mRNA and from rRNA depleted (strand specific) total RNA. ChIP-Seq profiling and RNA-Seq profiling on mouse naive ES cells

2012-04-26 | E-GEOD-23943 | biostudies-arrayexpress

Determination of the Lef1 regulated tanscriptome in differentiating ES cells

Project description:Lef1 is a critical transducer of the Wnt/beta-catenin signaling pathway that is essential for mesoderm differentiation in vertebrate embryos. We established a doxycycline inducible ES cell line to over-express Flag-tagged Lef1 in differentiating ES cells which have the capacity to form mesoderm cells in vitro. The goal of this study was to identify the genes/gene networks regulated by Lef1 to understand how it regulates mesoderm differentiation and to establish the Lef1-regulated, Wnt/beta-catenin transcriptome. Total RNA was extracted from ES cells after 3 days of differentiating following Lef1 over-expression from day 2 to 3. We compared the transcriptome of differentially expressed genes in untreated and doxycycline treated ES cells to identify Lef1 regulated genes.

2016-04-01 | E-GEOD-73083 | biostudies-arrayexpress

Determination of the Sp5 regulated transcriptome in differentiating ES cells

Project description:Sp5 is a target and critical transducer of the Wnt/beta-catenin signaling pathway and is essential for mesoderm differentiation in vertebrate embryos. We established a doxycycline inducible ES cell line to over-express Flag epitope-tagged Sp5 protein in differentiating ES cells which have the capacity to form mesoderm cells in vitro. The goal of this study was to identify the genes/gene networks regulated by Sp5 to understand how it regulates mesoderm differentiation by identifying important target genes which may mediate its activity. Total RNA was extracted from ES cells after 3 days of differentiating following F-Sp5 over-expression from day 2 to 3. We compared the transcriptome of differentially expressed genes between untreated (minus) and doxycycline treated (plus) ES cells to identify Sp5 regulated genes.

2016-04-01 | E-GEOD-73082 | biostudies-arrayexpress

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