Abstract

Accurate functional annotation of regulatory elements is essential for understanding global gene regulation. Here, we report a genome-wide map of 827,000 transcription factor binding sites in human lymphoblastoid cell lines, which is comprised of sites corresponding to 239 position weight matrices of known transcription factor binding motifs, and 49 novel sequence motifs. To generate this map, we developed a probabilistic framework that integrates cell- or tissue-specific experimental data such as histone modifications and DNase I cleavage patterns with genomic information such as gene annotation and evolutionary conservation. Comparison to empirical ChIP-seq data suggests that our method is highly accurate yet has the advantage of targeting many factors in a single assay. We anticipate that this approach will be a valuable tool for genome-wide studies of gene regulation in a wide variety of cell types or tissues under diverse conditions.

Keywords

BiologyDNA binding siteComputational biologyTranscription factorGeneticsChIP-sequencingHuman genomeChromatin immunoprecipitationChromatinENCODEGenomeGeneHistoneGene expressionPromoterChromatin remodeling

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Publication Info

Year
2010
Type
article
Volume
21
Issue
3
Pages
447-455
Citations
570
Access
Closed

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Roger Piqué-Regi, Jacob F. Degner, Athma A. Pai et al. (2010). Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Research , 21 (3) , 447-455. https://doi.org/10.1101/gr.112623.110

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DOI
10.1101/gr.112623.110