Defining bacterial regulons using ChIP-seq

•ChIP-seq is a powerful method for identifying transcription factor binding in vivo.•Correlation of ChIP-seq and transcriptomic data can identify bacterial regulons.•An overview of ChIP-seq methodology and data analysis in bacteria is provided.•ChIP-seq sample preparation, data analysis, and computational analyses are reviewed. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a powerful method that identifies protein–DNA binding sites in vivo. Recent studies have illustrated the value of ChIP-seq in studying transcription factor binding in various bacterial species under a variety of growth conditions. These results show that in addition to identifying binding sites, correlation of ChIP-seq data with expression data can reveal important information about bacterial regulons and regulatory networks. In this chapter, we provide an overview of the current state of knowledge about ChIP-seq methodology in bacteria, from sample preparation to raw data analysis. We also describe visualization and various bioinformatic analyses of processed ChIP-seq data.