Characterization of DNA-Protein Interactions: Design and Analysis of ChIP-Seq Experiments

Abstract

Within the last decade, advances in high-throughput sequencing have enabled extensive research into protein-DNA interactions on a genomic scale. These interac-tions include the binding of transcription factor proteins to localized positions on DNA, as well as proteins involved in other aspects of transcriptiona l regulation (e.g., methylases, acetylases) and in transcription itself (polymerases, etc.). The same methods can further be used to ascertain relevant aspects of chromatin state involved in transcriptional regulation, most notably key histone " marks " (including methylation and acetylation). The primary experimental method used is chromatin immunoprecipitation fol-lowed by sequencing, or ChIP-seq. While ChIP assays have been utilized for some time, modern high-throughput sequencing has enabled the entire genome (rather than just a small number of genes or genomic loci) to be interr ogated in a single experiment. Figure 10.1 , generated by the ENCODE project (ENCODE Project Consortium 2011), shows the high-level picture of regulatory elements in the genome, including the aspects that may be examined using ChIP-seq. This chapter describes how to design, implement, and analyze ChIP-seq experiments to success-fully address a range of biological questions involving DNA-protein interactions and transcriptional regulation.