Rada-Iglesias, A. et al. Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays. Hum. Mol. Genet. 14, 3435-3447

Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden.
Human Molecular Genetics (Impact Factor: 6.39). 12/2005; 14(22):3435-47. DOI: 10.1093/hmg/ddi378
Source: PubMed


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.

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Available from: Jan Komorowski, Dec 13, 2013
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    • "A down-regulation of histone acetylation after HDAC inhibitor treatment may seem unexpected, but we made the same observation on other class II genes when using the HDAC inhibitor trichostatin A [13]. Moreover, the HDAC inhibitor butyrate was reported to counteract with the 1α,25(OH) 2 D 3 response of the VDR target genes osteocalcin [46] and also showed genome-wide at least as many down-regulated than up-regulated genes [47]. Moreover, contrary to expectations HDAC inhibition seems not to cause global histone acetylation at gene regulatory regions [48] [49]. "
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    • "Over the last years, a variety of experimental approaches was introduced to detect TF interactions controlling tissue gene expression. Among the most used technologies, gel retardation assays [4], genomic microarrays [5], or chromatin immunoprecipitation followed by microarrays or high-throughput sequencing [6,7] were used to construct transcriptional models in different tissues. However, these studies are able to detect TF interactions on a limited scale since they treat each TF separately. "
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    • "ChIP on patient samples and HT29 cells were performed as previously described [13,54]. DNA amplification, fragmentation, labelling and hybridizations of ChIP and input DNAs were performed according to Affymetrix recommendations and basically as previously described [13], using Affymetrix GeneChip Human Promoter 1.0 arrays, which cover approximately from 7.5 kb upstream to 2.45 kb downstream of transcription start sites for over 25,500 human promoters. "
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