Genomics

Dataset Information

102

Vascular histone deacetylation by pharmacological HDAC inhibition [SAHA, ChIP-seq]


ABSTRACT: HDAC inhibitors are thought to regulate gene expression by post-translational modification of histone as well as non-histone proteins. Often studied at single loci, increased histone acetylation is the paradigmatic mechanism of action, however, little is known of the extent of genome-wide changes of the mammalian genome when stimulated by the hydroxamic acids, TSA and SAHA. In primary human vascular endothelial cells we map the chromatin modifications, histone H3 acetylation of lysine 9 and 14 (H3K9/14ac) using chromatin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq). Since acetylation mediated gene expression is often associated with modification of other lysine residues we also examined H3K4me3 and H3K9me3 as well as changes in CpG methylation (CpG-seq). Genome-wide mRNA sequencing indicates the differential expression of about 30% of genes, with almost equal numbers being up- and down- regulated. We observe deacetylation conferred by TSA and SAHA that are associated with decreased gene expression. Histone deacetylation is associated with the loss of p300/CBP binding at gene promoters. This study provides an important framework for HDAC inhibitor function in vascular biology and a comprehensive description of genome-wide deacetylation. HAEC ChIP-seq profiles for 3 histone marks of SAHA treated and control samples were generated by deep sequencing, in triplicate, using Illumina GAIIx.

ORGANISM(S): Homo sapiens  

SUBMITTER: Assam El-Osta  Tom C Karagiannis   Aneta Balcerczyk   Jun Okabe   Harikrishnan Kn   Haloom Rafehi   Sebastian Lunke   Xiao-Jun Du   Samuel T Keating   Ishant Khurana   Abdul W Khan   Antony Kaspi   Izhak Haviv   Mark Ziemann   Jenny Ooi   Lisa Chang    

PROVIDER: E-GEOD-54909 | ArrayExpress | 2014-05-06

SECONDARY ACCESSION(S): GSE54909SRP037715PRJNA238015

REPOSITORIES: GEO, ArrayExpress, ENA

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