Nucleic Acids Research Advance Access published online on October 12, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp823
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Genomics |
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing
1Department of Genetics and Pathology, Rudbeck Laboratory, SE-751 85 Uppsala, Sweden, 2Linnaeus Centre for Bioinformatics, Uppsala, Sweden and 3Interdisciplinary Centre for Mathematical and Computer Modelling, Warsaw University, Poland
*To whom correspondence should be addressed. Tel: +46-18-4714076; Fax: +46-18-4714808; Email: claes.wadelius{at}genpat.uu.se
Received June 12, 2009. Revised September 11, 2009. Accepted September 17, 2009.
Gene expression is regulated by combinations of transcription factors, which can be mapped to regulatory elements on a genome-wide scale using ChIP experiments. In a previous ChIP-chip study of USF1 and USF2 we found evidence also of binding of GABP, FOXA2 and HNF4a within the enriched regions. Here, we have applied ChIP-seq for these transcription factors and identified 3064 peaks of enrichment for GABP, 7266 for FOXA2 and 18783 for HNF4a. Distal elements with USF2 signal was frequently bound also by HNF4a and FOXA2. GABP peaks were found at transcription start sites, whereas 94% of FOXA2 and 90% of HNF4a peaks were located at other positions. We developed a method to accurately define TFBS within peaks, and found the predicted sites to have an elevated conservation level compared to peak centers; however the majority of bindings were not evolutionary conserved. An interaction between HNF4a and GABP was seen at TSS, with one-third of the HNF4a positive promoters being bound also by GABP, and this interaction was verified by co-immunoprecipitations.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.