title: Defining bacterial regulons using ChIP-seq.
abstract: 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.
authors.affiliation: Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI 53706, USA; Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, WI 53706, USA.
authors.forename: Kevin S
authors.initials: KS
authors.lastname: Myers
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
authors.forename: Dan M
authors.initials: DM
authors.lastname: Park
authors.affiliation: Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA.
authors.forename: Nicole A
authors.initials: NA
authors.lastname: Beauchene
authors.affiliation: Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA; Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, WI 53706, USA. Electronic address: pjkiley@wisc.edu.
authors.forename: Patricia J
authors.initials: PJ
authors.lastname: Kiley
mesh_terms: D001419:Bacteria / Q000235:genetics; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008967:Molecular Biology / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D018085:Regulon / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004268:DNA-Binding Proteins
keywords: Bacterial regulons; Bioinformatics analysis of genomic data; ChIP-seq; Genome-wide analysis; Systems biology; Transcription factor binding sites; Transcriptional regulation