Identification and characterization of transcription networks in environmentally significant species

Lawrence, Charles E. ; McCue, Lee Ann

Health Research Inc., Rensselaer, NY 12144

关键词: Abundance;    Molecular Biology;    Genes;    Functionals;    Bioinformatics;   

DOI  :  10.2172/860762
RP-ID  :  DOE/ER/63204-1
RP-ID  :  FG02-01ER63204
RP-ID  :  860762

美国|英语

来源: UNT Digital Library

【 摘 要 】

Understanding the regulation of gene expression, transcription regulation in particular, is one of the grand challenges of molecular biology. Transcription regulation is arguably the most important foundation of cellular function, since it exerts the most fundamental control of the abundance of virtually all of a cell's functional macromolecules. Nevertheless, this process, perhaps because of its difficulty, has been the subject of only a limited number of genomic level analyses. We have undertaken bioinformatics projects to address this issue by developing (1) a cross-species comparison method (i.e. phylogenetic footprinting) for the identification of transcription factor binding sites, (2) a Bayesian clustering method to identify regulons, (3) an improved scanning algorithm that uses a position weight matrix and several related species sequence data to locate transcription factor binding sites, and (4) a method to predict cognate binding sites for transcription factors of unknown specificity. These bioinformatics methods were developed using the model proteobacterium Escherichia coli, with further applications to the genomes of environmentally significant microbes (Rhodopseudomonas palustris, Shewanella oneidensis) in later years of the grant.