The University of California at Davis has been awarded a grant to evaluate Stress-Induced DNA Duplex Destabilization (SIDD) in Microbial genomes as a means to identify and analyze regulatory regions in the DNA. It will analyze all fully sequenced prokaryotic and archaeal genomes and determine the associations between SIDD sites and known regulatory sites. In particular, (1) destabilized regions will be computed for all known microbial genomes; (2) these regions will be compared with experimentally verified promoter regions, and the roles of destabilization for a variety of regulatory process assessed; (3) the relationship between destabilized regions and gene expression will be analyzed; (4) candidate regions for binding-induced transmission of destabilization will be computed for E. coli and other model organisms for a number of regulatory binding proteins, and (5) SIDD will be used to develop a method to predict promoter sites and replication origins and to identify small functional RNA genes locations.
