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

Background: Transcriptional regulation in eukaryotes often involves multiple transcription factors binding to the same transcription control region, 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 determination of conserved sequences (often known as phylogenetic footprinting) has identified individual transcription factor binding sites. We extend this concept of functional conservation to higher-order features of transcription control regions. 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 989 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 correspo...

• Type: Conference
• Year: 2003
• Where: RECOMB
• Authors: Derek Y. Chiang, Alan M. Moses, Manolis Kamvysselis, Eric S. Lander, Michael B. Eisen
• Keywords: Computational Biology, Factor Binding Sites, Informative Regression Models, RECOMB 2003, Transcription Control Regions