Detecting DNA-protein interactions in living cells--ChIP approach.

ABSTRACT

DNA-binding proteins play a critical role in many major cellular processes. The immunoprecipitation of protein complexes with associated DNA fragments, termed chromatin immunoprecipitation or ChIP, allows for the analysis of the binding of protein factors in their natural environment. It evolved from a confirmation assay to a discovery tool that really changed our understanding of the biology of living cells. With the widespread use of next-generation high-throughput sequencing technologies, factor binding can not only be assessed in an unbiased and genome-wide manner but can also be predicted and linked to gene expression and chromatin structure. This review summarizes the current advances of the ChIP-based approaches to decipher gene regulatory and epigenetic network in the cells. The limitations of the method are discussed and the future ChIP-based developments are explored.