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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Zhang C,Xuan Z,Otto S,Hover JR,McCorkle SR,Mandel G,Zhang MQdoi
10.1093/nar/gkl248subject
Has Abstractpub_date
2006-05-02 00:00:00pages
2238-46issue
8eissn
0305-1048issn
1362-4962pii
34/8/2238journal_volume
34pub_type
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