Functional Analysis of DNA and Chromatin

Abstract

Chromatin plays important functions in regulating many biological processes, including DNA transcription, replication, and repair. The use of chromatin immunoprecipitation (ChIP) assays has contributed enor- mously to identify interactions between DNA and a wide range of nuclear proteins including histones and their different posttranslational modifi cations as well as a variety of transcription factors. ChIP assays have been successfully used to map histone modifi cations and histone variants, as well as binding of transcription factors and chromatin-modifying complexes in both, specifi c candidate loci and the entire genome. In this chapter, we provide a brief review of the variations in ChIP assays and a detailed explanation of the basic standard ChIP protocol.