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Distance conservation of transcription regulatory motifs in human promoters

Paper ID Volume ID Publish Year Pages File Format Full-Text
15367 1407 2008 5 PDF Available
Title
Distance conservation of transcription regulatory motifs in human promoters
Abstract

To understanding the interaction network among transcription-regulation elements in human is an immediate challenge for modern molecular biology. Here a central problem is how to extract evolutionary information and search the evolutionary conservation from the comparison of promoters of closely related species. Through the comparative studies of k-mer distribution in human and mouse transcription factor binding site (TFBS) sequences we have discovered that the average distance between a pair of transcription regulatory 7-mer motifs is conservative in human–mouse promoters. The distance conservation is a new kind of evolutionary conservation, not based on the strict location of bases in genome sequence. By utilizing the conservation of k-mer distance it will be helpful to propose a non-alignment-based approach for fast genome-wide discovery of transcription regulatory motifs. We demonstrated the distance conservation by genome-wide searching of conservative regulatory 7-mer motifs with successful rate 90%. Then, after defining human–mouse pair-distance divergence parameter we studied the tissue-specific motif pairs and found that the parameter for motif pairs is 11–16 times smaller than for their controls for 28 tissues and these pairs can be clearly differentiated on two-dimensional parameter plane. Finally, the mechanism of distance conservation was discussed briefly which is supposed to be related to the module structure of TFBSs.

Keywords
Distance conservation; Transcription regulatory motifs; Heptamer motifs; Tissue-specific motif pairs; Human promoters
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Distance conservation of transcription regulatory motifs in human promoters
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 32, Issue 6, December 2008, Pages 433–437
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us