ChIP-Seq using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites

Much of eukaryotic gene regulation is mediated by binding of transcription factors near or within their target genes. Transcription factor binding sites (TFBS) are often identified globally using chromatin immunoprecipitation (ChIP) in which specific protein-DNA interactions are isolated using an antibody against the factor of interest. Coupling ChIP with high-throughput DNA sequencing allows identification of TFBS in a direct, unbiased fashion; this technique is termed ChIP-Sequencing (ChIP-Seq). In this chapter, we describe the yeast ChIP-Seq procedure, including the protocols for ChIP, input DNA preparation, and Illumina DNA sequencing library preparation. Descriptions of Illumina sequencing and data processing and analysis are also included. The use of multiplex short-read sequencing (i.e., barcoding) enables the analysis of many ChIP samples simultaneously, which is especially valuable for organisms with small genomes such as yeast.