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

Hum Mol Genet. 2005 Nov 15;14(22):3435-47. doi: 10.1093/hmg/ddi378. Epub 2005 Oct 12.


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 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • 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, Genetic
  • Sequence Analysis, DNA
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Upstream Stimulatory Factors / metabolism


  • Chromatin
  • HNF4A protein, human
  • Hepatocyte Nuclear Factor 4
  • Histones
  • Transcription Factors
  • USF1 protein, human
  • Upstream Stimulatory Factors
  • Hepatocyte Nuclear Factor 3-beta