Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Chromatin immunoprecipitation of human cell line HEPG2 to identify liver specific transcription factor binding sites

ABSTRACT: Identification of liver transcription factors binding sites by ChIP-chip using HepG2 cells. Inference of binding sites at base pair resolution was achieved by using bioinformatic tools on the generated data sets.

INSTRUMENT(S): Axon GenePix4000B

ORGANISM(S): Homo sapiens

SUBMITTER: Claes Wadelius

PROVIDER: E-MEXP-452 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays.

Rada-Iglesias Alvaro A Wallerman Ola O Koch Christoph C Ameur Adam A Enroth Stefan S Clelland Gayle G Wester Kenneth K Wilcox Sarah S Dovey Oliver M OM Ellis Peter D PD Wraight Vicki L VL James Keith K Andrews Rob R Langford Cordelia C Dhami Pawandeep P Carter Nigel N Vetrie David D Pontén Fredrik F Komorowski Jan J Dunham Ian I Wadelius Claes C

Human molecular genetics 20051012 22

We present a detailed in vivo characterization of hepatocyte transcriptional regulation in HepG2 cells, using chromatin immunoprecipitation and detection on PCR fragment-based genomic tiling path arrays covering the encyclopedia of DNA element (ENCODE) regions. Our data suggest that HNF-4alpha and HNF-3beta, which were commonly bound to distal regulatory elements, may cooperate in the regulation of a large fraction of the liver transcriptome and that both HNF-4alpha and USF1 may promote H3 acety ...[more]

PMID: 16221759

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Project description:Transcript elongation by RNA polymerase II (RNAPII) is accompanied by conserved patterns of histone modification within transcribed regions, but it remains uncertain how these modifications influence, or are influenced by, properties of the elongation complex. Here we establish an intimate link between Cdk9, the kinase component of positive transcription elongation factor b (P-TEFb), and mono-ubiquitylation of histone H2B (H2Bub1), in the fission yeast Schizosaccharomyces pombe. Mutations that impair Cdk9 function reduce H2Bub1 levels in vivo. Conversely, mutations that prevent H2Bub1 decrease phosphorylation of elongation factor subunit Spt5, a sensitive and specific indicator of Cdk9 activity. Chromatin immunoprecipitation (ChIP) analysis suggests this is due to impaired Cdk9 recruitment to H2Bub1-deficient chromatin. P-TEFb and H2Bub1 pathways also interact genetically: mutation of the histone H2B ubiquitin-acceptor residue decreases the requirement for Cdk9 activity in vivo, and multiple cdk9 mutations suppress morphological defects of H2Bub1-deficient strains. Moreover, H2Bub1 loss causes redistribution of transcribing RNAPII on chromatin that is corrected by a hypomorphic cdk9 mutation. Therefore, whereas mutual dependence of Spt5 phosphorylation and H2Bub1 suggests positive feedback between P-TEFb and the ubiquitylation machinery, mutual suppression by cdk9 and H2Bub1-pathway mutations indicates an antagonistic relationship, whereby the activities must be balanced to properly regulate elongation. In order to study the genome-wide localization of H2Bub1 in Schizosaccharomyces pombe, H2Bub1, H2B-Flag as well as RNAPII (along with associated DNA sequences) were immunoprecipitated using repectively anti-H2Bub1, anti-Flag and anti-8WG16 antibodies. The ChIPs were performed in duplicate from WT cells as well as in the H2B-K119R mutant. The extracted DNA was hybridized to a DNA microarray containing an average of 4 probes per kilobase across the whole yeast genome. The combined datasets are available in the supplemental files of the related publication.

Dataset Information

Chromatin immunoprecipitation of human cell line HEPG2 to identify liver specific transcription factor binding sites

Publications

Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays.

Similar Datasets

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