A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1.
Advances in high-throughput technologies, such as ChIP-chip, and the completion of human and mouse genomic sequences now allow analysis of the mechanisms of gene regulation on a systems level. In this study, we have developed a computational genomics approach (termed ChIPModules), which begins with experimentally determined binding sites and integrates positional weight matrices constructed from transcription factor binding sites, a comparative genomics approach, and statistical learning methods to identify transcriptional regulatory modules. We began with E2F1 binding site information obtained from ChIP-chip analyses of ENCODE regions, from both HeLa and MCF7 cells. Our approach not only distinguished targets from nontargets with a high specificity, but it also identified five regulatory modules for E2F1. One of the identified modules predicted a colocalization of E2F1 and AP-2alpha on a set of target promoters with an intersite distance of <270 bp. We tested this prediction using ChIP-chip assays with arrays containing approximately 14,000 human promoters. We found that both E2F1 and AP-2alpha bind within the predicted distance to a large number of human promoters, demonstrating the strength of our sequence-based, unbiased, and universal protocol. Finally, we have used our ChIPModules approach to develop a database that includes thousands of computationally identified and/or experimentally verified E2F1 target promoters.
Jin
Victor X
VX
Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA.
Rabinovich
Alina
A
Squazzo
Sharon L
SL
Green
Roland
R
Farnham
Peggy J
PJ
D020029:Base Pairing; D001665:Binding Sites; D001943:Breast Neoplasms / Q000473:pathology; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology; D050687:E2F1 Transcription Factor / Q000235:genetics / Q000378:metabolism*; D023281:Genomics; D006367:HeLa Cells; D006801:Humans; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D012372:ROC Curve; D012045:Regulatory Sequences, Nucleic Acid; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012984:Software
D050687:E2F1 Transcription Factor