A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data - A case study using E2F1

Victor X. Jin, Alina Rabinovich, Sharon L. Squazzo, Roland Green, Peggy J. Farnham

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

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-2α on a set of target promoters with an intersite distance of <270 bp. We tested this prediction using ChIP-chip assays with arrays containing ∼14,000 human promoters. We found that both E2F1 and AP-2α 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.

Original languageEnglish (US)
Pages (from-to)1585-1595
Number of pages11
JournalGenome Research
Volume16
Issue number12
DOIs
StatePublished - Dec 2006

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Chromatin Immunoprecipitation
Genomics
Binding Sites
MCF-7 Cells
HeLa Cells
Transcription Factors
Learning
Databases
Technology
Weights and Measures
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data - A case study using E2F1. / Jin, Victor X.; Rabinovich, Alina; Squazzo, Sharon L.; Green, Roland; Farnham, Peggy J.

In: Genome Research, Vol. 16, No. 12, 12.2006, p. 1585-1595.

Research output: Contribution to journalArticle

Jin, Victor X. ; Rabinovich, Alina ; Squazzo, Sharon L. ; Green, Roland ; Farnham, Peggy J. / A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data - A case study using E2F1. In: Genome Research. 2006 ; Vol. 16, No. 12. pp. 1585-1595.
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