Studying histone modifications and their genomic functions by employing chromatin immunoprecipitation and immunoblotting.

Histones are one of the most abundant and highly conserved proteins in eukaryotes. Apart from serving as structural entities for orderly compaction of genomes, they play an instrumental role in the regulation of many important biological processes involving DNA such as transcription, DNA repair, and the cell cycle. Histone modifications have been implicated in maintaining the transcriptionally poised state of important genesin embryonic stem cells. Histone modifications are believed to be responsible for compartmentalization of chromatin into active and inactive domains. Hence, the tools and techniques required for studying these proteins are of utmost importance to biologists. This chapter provides a brief review of the posttranslational modifications of the N-terminal tails of histones and their biological roles, followed by step-by-step protocols for the most common techniques employed to study them. Here, we describe chromatin immunoprecipitation (ChIP) for studying the genomic functions of the most widely studied histone modifications, namely, histone H3 lysine 9 acetylation and histone H3 lysine 9 trimethylation that are typically associated with transcriptional activation and repression, respectively. Special emphasis has been given on the method of preparation of sonicated chromatin prior to immunoprecipitation since this single step affects the success of ChIP greatly and is often poorly described in published protocols. Protocol for histone isolation by acid-extraction and detection by Coomassie staining has also been described. We also describe the protocol for immunoblot analysis of histones using antibodies against key histone modifications. This chapter will serve as a useful resource in the study of histones and their posttranslational modifications.