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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    ABSTRACT: The signaling cascade of the transcription factor vitamin D receptor (VDR) is triggered by its specific ligand 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3). In this study we demonstrate that in THP-1 human monocytic leukemia cells 87.4% of the 1,034 most prominent genome-wide VDR binding sites co-localize with loci of open chromatin. At 165 of them 1α,25(OH)2D3 strongly increases chromatin accessibility and has at further 217 sites weaker effects. Interestingly, VDR binding sites in 1α,25(OH)2D3-responsive chromatin regions are far more often composed of direct repeats with 3 intervening nucleotides (DR3s) than those in ligand insensitive regions. DR3-containing VDR sites are enriched in the neighborhood of genes that are involved in controling cellular growth, while non-DR3 VDR binding is often found close to genes related to immunity. At the example of six early VDR target genes we show that the slope of their 1α,25(OH)2D3-induced transcription correlates with the basal chromatin accessibility of their major VDR binding regions. However, the chromatin loci controlling these genes are indistinguishable in their VDR association kinetics. Taken together, ligand responsive chromatin loci represent dynamically regulated contact points of VDR with the genome, from where it controls early 1α,25(OH)2D3 target genes.
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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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    ABSTRACT: Tissue-specific gene expression is generally regulated by combinatorial interactions among transcription factors (TFs) which bind to the DNA. Despite this known fact, previous discoveries of the mechanism that controls gene expression usually consider only a single TF. We provide a prediction of interacting TFs in 22 human tissues based on their DNA-binding affinity in promoter regions. We analyze all possible pairs of 130 vertebrate TFs from the JASPAR database. First, all human promoter regions are scanned for single TF-DNA binding affinities with TRAP and for each TF a ranked list of all promoters ordered by the binding affinity is created. We then study the similarity of the ranked lists and detect candidates for TF-TF interaction by applying a partial independence test for multiway contingency tables. Our candidates are validated by both known protein-protein interactions (PPIs) and known gene regulation mechanisms in the selected tissue. We find that the known PPIs are significantly enriched in the groups of our predicted TF-TF interactions (2 and 7 times more common than expected by chance). In addition, the predicted interacting TFs for studied tissues (liver, muscle, hematopoietic stem cell) are supported in literature to be active regulators or to be expressed in the corresponding tissue. The findings from this study indicate that tissue-specific gene expression is regulated by one or two central regulators and a large number of TFs interacting with these central hubs. Our results are in agreement with recent experimental studies.
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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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