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Phylogenetically and spatially conserved word pairs associated with gene expression changes in yeasts

Content Provider	ACM Digital Library
Author	Eisen, Michael B. Lander, Eric S. Chiang, Derek Y. Kamvysselis, Manolis Moses, Alan M.
Abstract	Background. Transcriptional regulation in eukaryotes is often multifactorial, involving multiple transcription factors binding to the same transcription control region (e.g., upstream activating sequences and enhancers), and to understand the regulatory content of eukaryotic genomes it is necessary to consider the co-occurrence and spatial relationships of individual binding sites. The identification of sequences conserved among related species (often known as phylogenetic footprinting) has been successfully used to identify individual transcription factor binding sites. Here, we extend this concept of functional conservation to higher-order features of transcription control regions involved in the multifactorial control of gene expression.Results. We used the genome sequences of four yeast species of the genus Saccharomyces to identify sequences potentially involved in multifactorial control of gene expression. We found 1,117 potential regulatory "templates": pairs of hexameric sequences that are jointly conserved in transcription regulatory regions and also exhibit non-random relative spacing. Many of the individual sequences in these templates correspond to known transcription factor binding sites, and the sets of genes containing a particular template in their transcription control regions tend to be differentially expressed in conditions where the corresponding transcription factors are known to be active.Conclusions. The incorporation of both joint conservation and spacing constraints of sequence pairs predicts groups of target genes that were specific for common patterns of gene expression. Our work suggests that positional information, especially the relative spacing between transcription factor binding sites, may represent a common organizing principle of transcription control regions.
Starting Page	84
Ending Page	93
Page Count	10
File Format	PDF
ISBN	1581136358
DOI	10.1145/640075.640085
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2003-04-10
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Comparative genomics Phylogenetic footprinting Multifactorial regulation Promoter structure Transcription regulation
Content Type	Text
Resource Type	Article

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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