Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

H3K27Ac and H3K4me1 ChIP-seq in Rex1GFPd2 mouse embryonic stem cell line

ABSTRACT: Chromatin immunoprecipitation using H3K27Ac and H3K4me1 antibodies in Rex1GFPd2 mouse ES cells (parental line; E14Tg2a)

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: Ian Donaldson

PROVIDER: E-MTAB-2282 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Otx2 and Oct4 drive early enhancer activation during embryonic stem cell transition from naive pluripotency.

Yang Shen-Hsi SH Kalkan Tüzer T Morissroe Claire C Marks Hendrik H Stunnenberg Hendrik H Smith Austin A Sharrocks Andrew D AD

Cell reports 20140612 6

Embryonic stem cells (ESCs) are unique in that they have the capacity to differentiate into all of the cell types in the body. We know a lot about the complex transcriptional control circuits that maintain the naive pluripotent state under self-renewing conditions but comparatively less about how cells exit from this state in response to differentiation stimuli. Here, we examined the role of Otx2 in this process in mouse ESCs and demonstrate that it plays a leading role in remodeling the gene re ...[more]

PMID: 24931607

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Project description:Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II A common landmark of activated genes is the presence of trimethylation on lysine 4 of histone H3 (H3K4) at promoter regions. The Set1/COMPASS was the founding member and the only H3K4 methylases in S. cerevisiae, however, in mammals at least six H3K4 methylases Set1A/B and MLL1-4 are found in COMPASS-like complexes capable of methylating H3K4. To gain further insight into the different roles and functional targets for the H3K4 methylases, we have undertaken a genome-wide analysis of H3K4 methylation pattern in wild-type Mll1+/+ and Mll1-/- mouse fibroblasts (MEFs). We found that Mll1 is required for the H3K4 trimethylation of less than 5% of promoters carrying this modification. Many of these genes, which include developmental regulators such as Hox genes show decreased levels of RNA polymerase II recruitment and expression concomitant with the loss of H3K4 methylation. Although Mll1 is only required for the methylation of a subset of Hox genes, Menin, a component of the Mll1 and Mll2 complexes, is required for the overwhelming majority of H3K4 methylation at Hox loci. However, the loss of MLL3/4 and/or the Set1 complexes have little to no effect on the Hox loci H3K4 methylation or expression levels in these MEFs. Together these data provide insight into redundancy and specialization of COMPASS-like complexes in mammals and provide evidence on a possible role for Mll1-mediated H3K4 methylation in the regulation of transcriptional initiation. Chromatin Immunoprecipitation was performed with antibodies for histone 3 lysine 4 trimethylation, histone 3, and PolII in Mll1+/+ and Mll1-/- mouse embryonic fibroblasts. DNA was hybridized to a custom Agilent tiling array (4x44k format) that covers three of the hox regions (A,B,D) and a collection of other genes.

Dataset Information

H3K27Ac and H3K4me1 ChIP-seq in Rex1GFPd2 mouse embryonic stem cell line

Publications

Otx2 and Oct4 drive early enhancer activation during embryonic stem cell transition from naive pluripotency.

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