Analysis of ChIP-Seq data identifies CzcR regulon

Purpose:To identify the direct targets and regulatory mechanism of CzcR in Pseudomonas aeruginosa, we performed chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (Seq). Methods: In the experiment, chromatin bound CzcR 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 108 enriched loci (p-value≤1e-5; fold enrichment>1) containing CzcR binding peak in the P. aeruginosa genome. In accordance with the previous studies, oprD, phzA1 promoters were significantly enriched compared to input DNA (80, 76-fold, respectively). Examination of 3 samples of pseudomonas aeruginosa