A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome

Zhang, C., Xuan, Z., Otto, S., Hover, J. R., McCorkle, S. R., Mandel, G., Zhang, M. Q. (2006) A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic Acids Res, 34 (8). pp. 2238-46. ISSN 1362-4962 (Electronic)

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URL: https://www.ncbi.nlm.nih.gov/pubmed/16670430
DOI: 10.1093/nar/gkl248

Abstract

Transcription factor binding sites (TFBSs) are short DNA sequences interacting with transcription factors (TFs), which regulate gene expression. Due to the relatively short length of such binding sites, it is largely unclear how the specificity of protein-DNA interaction is achieved. Here, we have performed a genome-wide analysis of TFBS-like sequences for the transcriptional repressor, RE1 Silencing Transcription Factor (REST), as well as for several other representative mammalian TFs (c-myc, p53, HNF-1 and CREB). We find a nonrandom distribution of inexact sites for these TFs, referred to as highly-degenerate TFBSs, that are enriched around the cognate binding sites. Comparisons among human, mouse and rat orthologous promoters reveal that these highly-degenerate sites are conserved significantly more than expected by random chance, suggesting their positive selection during evolution. We propose that this arrangement provides a favorable genomic landscape for functional target site selection.

Item Type: Paper
Uncontrolled Keywords: Animals Base Sequence Binding Sites Conserved Sequence Genomics Humans Mice Promoter Regions (Genetics) Rats Repressor Proteins/metabolism Transcription Factors/ metabolism
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > promoter
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > sDNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date: 2006
Date Deposited: 06 Dec 2011 16:50
Last Modified: 08 Nov 2017 15:33
PMCID: PMC1456330
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22949

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