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PMID: 10734201 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Discovering regulatory elements in non-coding sequences by analysis of spaced dyads.

Nucleic acids research ·Vol. 28 ·No. 8 ·2000-04-15 ·Pages 1808-18

van Helden J, Rios AF, Collado-Vides J

Abstract

The application of microarray and related technologies is currently generating a systematic catalog of the transcriptional response of any single gene to a multiplicity of experimental conditions. Clustering genes according to the similarity of their transcriptional response provides a direct hint to the regulons of the different transcription factors, many of which have still not been characterized. We have developed a new method for deciphering the mechanism underlying the common transcriptional response of a set of genes, i.e. discovering cis -acting regulatory elements from a set of unaligned upstream sequences. This method, called dyad analysis, is based on the observation that many regulatory sites consist of a pair of highly conserved trinucleotides, spaced by a non-conserved region of fixed width. The approach is to count the number of occurrences of each possible spaced pair of trinucleotides, and to assess its statistical significance. The method is highly efficient in the detection of sites bound by C(6)Zn(2)binuclear cluster proteins, as well as other transcription factors. In addition, we show that the dyad and single-word analyses are efficient for the detection of regulatory patterns in gene clusters from DNA chip experiments. In combination, these programs should provide a fast and efficient way to discover new regulatory sites for as yet unknown transcription factors.

MeSH Terms
Base Sequence DNA Database Management Systems Gene Expression Regulation Regulatory Sequences, Nucleic Acid Transcription Factors/genetics
Chemicals
Transcription Factors DNA
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
van Helden J
Unité de Conformation des Macromolécules Biologiques, Université Libre de Bruxelles, CP 160/16, 50 av. F. D. Roosevelt, B-1050 Bruxelles, Belgium. [email protected]
Rios A F
Collado-Vides J
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/28.8.1808
Email
[email protected]
Published
2000-04-15
Pages
1808-18
Language
English
Region
England
NLM ID
0411011
PMCID
PMC102821
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/28.8.1808 PMC Full Text View journal details
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