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

• 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-4α and HNF-3β, 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-4α and USF1 may promote H3 acetylation to many of their targets. Importantly, bioinformatic analysis of the sequences bound by each transcription factor (TF) shows an over-representation of motifs highly similar to the in vitro established consensus sequences. On the basis of these data, we have inferred tentative binding sites at base pair resolution. Some of these sites have been previously found by in vitro analysis and some were verified in vitro in this study. Our data suggests that a similar approach could be used for the in vivo characterization of all predicted/uncharacterized TF and that the analysis could be scaled to the whole genome.

Nyckelord

Base Pairing/*genetics

Binding Sites/genetics

Cell Line; Tumor

Chromatin/*metabolism

Chromatin Immunoprecipitation/methods

Consensus Sequence

Genome; Human

Hepatocyte Nuclear Factor 3-beta/physiology

Hepatocyte Nuclear Factor 4/physiology

Hepatocytes/metabolism

Histones/metabolism

Humans

Metabolic Diseases/*metabolism

Oligonucleotide Array Sequence Analysis/methods

Promoter Regions (Genetics)

Research Support; N.I.H.; Extramural

Research Support; Non-U.S. Gov't

Sequence Analysis; DNA

Transcription Factors/genetics/*metabolism

Upstream Stimulatory Factors/metabolism

Publikations- och innehållstyp

ref (ämneskategori)

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