Analysis of ChIP-Seq data identifies BfmR regulon

Purpose:To identify the direct targets and regulatory mechanism of BfmR in Pseudomonas aeruginosa, we performed chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (Seq). Methods: In the experiment, chromatin bound BfmR was crosslinked, sheared, bound to antibody, nonspecific proteins and nucleic acids removed, purified and sequenced. The sequencing data were obtained from several independent ChIP samples and then located on the p. aeruginosa genome. The MACS (Model-based Analysis for ChIP-Seq) software was used to call peak for sequence reads. Results: We identified 141 enriched loci (p-value=1e-5; fold enrichment>3) containing BfmR binding peak in the P. aeruginosa genome. In accordance with the previous studies, bfmR, PA4103 promoters were significantly enriched compared to input DNA (49, 60-fold, respectively), had the highest degree of enrichment in all peaks. Overall design: Examination of 9 samples of pseudomonas aeruginosa