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Chromatin immunoprecipitation and DNAse I hypersensitive site mapping of mouse hematopoietic cell lines and tissue-types to identify histone modification and transcription factor binding sites

ABSTRACT: Histone modification and transcription factor ChIP-chip in hematopoietic cell lines and tissue-types

ORGANISM(S): Mus musculus

SUBMITTER: Josette-Renee Landry

PROVIDER: E-TABM-455 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Endoglin expression in blood and endothelium is differentially regulated by modular assembly of the Ets/Gata hemangioblast code.

Pimanda John E JE Chan Wan Y I WY Wilson Nicola K NK Smith Aileen M AM Kinston Sarah S Knezevic Kathy K Janes Mary E ME Landry Josette-Renée JR Kolb-Kokocinski Anja A Frampton Jonathan J Tannahill David D Ottersbach Katrin K Follows George A GA Lacaud Georges G Kouskoff Valerie V Göttgens Berthold B

Blood 20080919 12

Endoglin is an accessory receptor for TGF-beta signaling and is required for normal hemangioblast, early hematopoietic, and vascular development. We have previously shown that an upstream enhancer, Eng -8, together with the promoter region, mediates robust endothelial expression yet is inactive in blood. To identify hematopoietic regulatory elements, we used array-based methods to determine chromatin accessibility across the entire locus. Subsequent transgenic analysis of candidate elements show ...[more]

PMID: 18805961

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Chromatin immunoprecipitation of mouse hematopoietic cell lines and tissue-types to identify histone modification and transcription factor binding sites

Project description:Histone modification and transcription factor ChIP-chip in hematopoietic cell lines and tissue-types

2009-01-28 | E-TABM-431 | biostudies-arrayexpress

ChIP-chip by array of mouse cell lines and fresh tissue using anti-acetyl histone H3 antibody.

Project description:Immunoprecipitations were performed using anti-acetyl histone H3 antibody (Millipore, 06-599)

2011-04-07 | E-MEXP-2664 | biostudies-arrayexpress

ChIP-chip by array of mouse cell lines and fresh tissues using anti-H3 trimethyl lysine 4.

Project description:Immunoprecipitations were performed using anti-H3 trimethyl lysine 4 (Millipore, 04-745 and gift from Dr. L. OM-oM->M-^RNeill, Birmingham, UK)

2010-06-09 | E-MEXP-2665 | biostudies-arrayexpress

ChIP-chip by array of mouse haematopoietic and endothelial cell lines using an anti-H3 trimethyl lysine 4 antibody

Project description:chromatin immunoprecipitations were performed in mouse haematopoietic and endothelial cell lines using an anti-H3 trimethyl lysine 4 antibody

2011-09-06 | E-MEXP-2908 | biostudies-arrayexpress

ChIP-chip by array of mouse 416Bcell line using anti-PU.1 (Santa Cruz, sc-352X).

Project description:Immunoprecipitations were performed using anti-PU.1 (Santa Cruz, sc-352X)

2011-04-07 | E-MEXP-2666 | biostudies-arrayexpress

5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer [seq]

Project description:The discovery of cytosine hydroxymethylation (5-hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behavior in colon cancer. 5-hmC is globally reduced in proliferating cells such as colon tumors and the gut crypt progenitors, from which tumors can arise. Here, we show that colorectal tumors and cancer cells express Ten-Eleven Translocation (TET) transcripts at levels similar to normal tissues. Genome-wide analyses show that promoters marked by 5-hmC in normal tissue, and those identified as TET2 targets in colorectal cancer cells, are resistant to methylation gain in cancer. In vitro studies of TET2 in cancer cells confirm that these promoters are resistant to methylation gain independently of sustained TET2 expression. We also find that a considerable number of the methylation gain-resistant promoters marked by 5-hmC in normal colon overlap with those that are marked with poised bivalent histone modifications in embryonic stem cells. Together our results indicate that promoters that acquire 5-hmC upon normal colon differentiation are innately resistant to neoplastic hypermethylation by mechanisms that do not require high levels of 5-hmC in tumors. Our study highlights the potential of cytosine modifications as biomarkers of cancerous cell proliferation. 5 normal colon samples and 4 matching tumor samples were profiled for 5-hydroxymethylcytosine content genomewide using hmeDIP-seq. The colorectal cancer cell line HCT116 was profiled for binding of TET2 genomewide by chromatin immunoprecipitation sequencing (ChIP-seq).

2015-02-03 | E-GEOD-47590 | biostudies-arrayexpress

Scl specifies hemogenic endothelium and inhibits cardiogenesis via primed enhancers [RNA-seq]

Project description:Scl/Tal1 confers hemogenic competence and prevents cardiomyogenesis in embryonic endothelium. Here we show that Scl both directly activates a broad gene regulatory network required for hematopoietic stem/progenitor cell (HS/PC) development, and represses transcriptional regulators required for cardiogenesis. Cardiac repression occurs during a short developmental window through Scl binding to distant cardiac enhancers that harbor H3K4me1 at this stage. Scl binding to hematopoietic regulators extends throughout HS/PC and erythroid development and spreads from distant enhancers to promoters. Surprisingly, Scl complex partners Gata 1 and 2 are dispensable for hematopoietic versus cardiac specification and Scl binding to the majority of its target genes. Nevertheless, Gata factors co-operate with Scl to activate selected transcription factors to facilitate HS/PC emergence from hemogenic endothelium. These results uncover a dual function for Scl in dictating hematopoietic versus cardiac fate choice and suggest a mechanism by which lineage-specific bHLH factors direct the divergence of competing fates. Examination of Scl and Gata 1 & 2 target genes in ES cell derived day4.75 EB (embryoid body) Tie2+CD31+CD41- endothelial cells

2015-01-01 | E-GEOD-47083 | biostudies-arrayexpress

Genome-wide mapping of Mef2c-bound sites in early B-cell progenitors

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2015-12-14 | E-GEOD-73453 | biostudies-arrayexpress

ChIP-chip by array of human B-acute lymphoblastic leukaemia cells using AcH3, H3K4M3 and H3K27M3 antibodies

Project description:B-ALL Xenograft Histone Modification at BIM locus<br>The cells used are human B- acute lymphoblastic leukaemia cells that have been propagated in<br>NOD/SCID mice. B-ALL2 and B-ALL3 are cells from two different patients.<br><br>Normalized data files containing chromosome 2 data are available on the FTP site for this experiment in the E-MEXP-2814.additional.zip archive.

2011-06-14 | E-MEXP-2814 | biostudies-arrayexpress

H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction (I) [ChIP-Seq]

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