I propose to study three different areas of the transcriptional regulatory network in E. coli using genome-scale methods. Specifically, I will first determine the location of promoters throughout the genome by identifying RNA polymerase binding sites using chromatin immunoprecipitation and custom-designed microarrays (chlP-:hip). I will also study the effects of termination factor Rho on transcription profiles by constucting a :onditional lethal mutant and isolating RNA under permissive and non-permissive conditions. Thrid, I will study four uncharacterized transcription factors using a combination of bioinformatic analysis of existing data sets followed by microarray analysis. Knockout mutants will be constructed in the four genes to identify DOtential regulatory targets under informative conditions. Direct versus indirect effects will be distinguished by dentifying transcription factor binding sites using chlP-chip. Results generated by this work will expand our knowledge of the regulatory network in E. coli and provide training in the integration of diverse data types.
| Herring, Christopher D; Palsson, Bernhard O (2007) An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes. BMC Genomics 8:274 |
| Herring, Christopher D; Raghunathan, Anu; Honisch, Christiane et al. (2006) Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet 38:1406-12 |
