title: Mapping Transcription Regulatory Networks with ChIP-seq and RNA-seq.
abstract: Bacterial genomes encode numerous transcription factors, DNA-binding proteins that regulate transcription initiation. Identifying the regulatory targets of transcription factors is a major challenge of systems biology. Here I describe the use of two genome-scale approaches, ChIP-seq and RNA-seq, that are used to map transcription factor regulons. ChIP-seq maps the association of transcription factors with DNA, and RNA-seq determines changes in RNA levels associated with transcription factor perturbation. I discuss the strengths and weaknesses of these and related approaches, and I describe how ChIP-seq and RNA-seq can be combined to map individual transcription factor regulons and entire regulatory networks.
authors.affiliation: New York State Department of Health, Wadsworth Center, Albany, NY, 12208, USA. joseph.wade@health.ny.gov.|Department of Biomedical Sciences, University at Albany, Albany, NY, 12201, USA. joseph.wade@health.ny.gov.
authors.forename: Joseph T
authors.initials: JT
authors.lastname: Wade
mesh_terms: D001483:Base Sequence; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D058893:DNA Barcoding, Taxonomic; D053263:Gene Regulatory Networks; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA
keywords: ChIP-chip; ChIP-seq; Chromatin immunoprecipitation; Microarray; RNA-seq; Regulatory network; Transcription factor; Transcription profiling