High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites

Whitington, T, Perkins, A. C. and Bailey, T. L. (2009) High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Nucleic Acids Research, 37 1: 14-25. doi:10.1093/nar/gkn866


Author Whitington, T
Perkins, A. C.
Bailey, T. L.
Title High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
Publication date 2009-01-01
Year available 2008
Sub-type Article (original research)
DOI 10.1093/nar/gkn866
Open Access Status DOI
Volume 37
Issue 1
Start page 14
End page 25
Total pages 12
Place of publication Oxford , U.K.
Publisher Oxford University Press
Language eng
Subject C1
970106 Expanding Knowledge in the Biological Sciences
060405 Gene Expression (incl. Microarray and other genome-wide approaches)
Abstract In silico prediction of transcription factor binding sites (TFBSs) is central to the task of gene regulatory network elucidation. Genomic DNA sequence information provides a basis for these predictions, due to the sequence specificity of TF-binding events. However, DNA sequence alone is an impoverished source of information for the task of TFBS prediction in eukaryotes, as additional factors, such as chromatin structure regulate binding events. We show that incorporating high-throughput chromatin modification estimates can greatly improve the accuracy of in silico prediction of in vivo binding for a wide range of TFs in human and mouse. This improvement is superior to the improvement gained by equivalent use of either transcription start site proximity or phylogenetic conservation information. Importantly, predictions made with the use of chromatin structure information are tissue specific. This result supports the biological hypothesis that chromatin modulates TF binding to produce tissue-specific binding profiles in higher eukaryotes, and suggests that the use of chromatin modification information can lead to accurate tissue-specific transcriptional regulatory network elucidation.
Keyword EMBRYONIC STEM-CELLS
Q-Index Code C1
Q-Index Status Provisional Code
Additional Notes First available online November 6, 2008

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
 
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Created: Thu, 03 Sep 2009, 19:04:13 EST by Mr Andrew Martlew on behalf of Institute for Molecular Bioscience