Chromatin is the complex of genomic DNA and associated proteins in the nucleus. This higher ordered structure of DNA allows cells to package their DNA, provides a scaffold for cell division, and enables control of gene expression. Chromatin structure, bound by a dynamic repertoire of proteins, alternates between condensed heterochromatin and extended euchromatin.
Chromatin Immunoprecipitation (ChIP) is a powerful technique for mapping the in vivo distribution of proteins associated with chromosomal DNA. These proteins can be histone subunits and post-translational modifications or other chromatin associated proteins such as transcription factors, chromatin regulators, etc. Additionally, ChIP can be used to identify regions of the genome associated with these proteins, or conversely, to identify proteins associated with a particular region of the genome. ChIP methodology often involves protein-DNA and protein-protein cross-linking, fragmentation of the cross-linked chromatin, and subsequent immunoprecipitation of chromatin with an antibody specific to a target protein. The DNA fragments isolated in complex with the target protein can be identified by a variety of methods including PCR, DNA microarray and DNA sequencing.
Chromatin is the natural state of DNA in the nucleus, and all DNA-related processes function in chromatin rather than on naked DNA. Because transcriptional or post-transcriptional regulation on naked DNA can differ from that on assembled chromatin, it is crucial to have a reliable method for assembling and analyzing chromatin in vitro.