title: Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome.
abstract: The E2F family of transcription factors regulates basic cellular processes. Here, we take an unbiased approach towards identifying E2F1 target genes by examining localization of E2F1-binding sites using high-density oligonucleotide tiling arrays. To begin, we developed a statistically-based methodology for analysis of ChIP-chip data obtained from arrays that represent 30 Mb of the human genome. Using this methodology, we identified regions bound by E2F1, MYC, and RNA Polymerase II (POLR2A). We found a large number of binding sites for all three factors; extrapolation suggests there may be approximately 20,000-30,000 E2F1- and MYC-binding sites and approximately 12,000-17,000 active promoters in HeLa cells. In contrast to our results for MYC, we find that the majority of E2F1-binding sites (>80%) are located in core promoters and that 50% of the sites overlap transcription starts. Only a small fraction of E2F1 sites possess the canonical binding motif. Surprisingly, we found that approximately 30% of genes in the 30-Mb region possessed an E2F1 binding site in a core promoter and E2F1 was bound near to 83% of POLR2A-bound sites. To determine if these results were representative of the entire human genome, we performed ChIP-chip analyses of approximately 24,000 promoters and confirmed that greater than 20% of the promoters were bound by E2F1. Our results suggest that E2F1 is recruited to promoters via a method distinct from recognition of the known consensus site and point toward a new understanding of E2F1 as a factor that contributes to the regulation of a large fraction of human genes.
authors.affiliation: Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Bieda
authors.forename: Xiaoqin
authors.initials: X
authors.lastname: Xu
authors.forename: Michael A
authors.initials: MA
authors.lastname: Singer
authors.forename: Roland
authors.initials: R
authors.lastname: Green
authors.forename: Peggy J
authors.initials: PJ
authors.lastname: Farnham
mesh_terms: D001665:Binding Sites; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D002891:Chromosomes, Human, Pair 21; D003627:Data Interpretation, Statistical; D050687:E2F1 Transcription Factor / Q000235:genetics / Q000378:metabolism*; D015894:Genome, Human; D006367:HeLa Cells; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D011485:Protein Binding
chemical_list: D050687:E2F1 Transcription Factor