Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation

Our understanding of the significance of interactions of proteins with DNA in the context of gene expression, cell differentiation or to some extent disease has immensely been enhanced by the advent of chromatin immunoprecipitation (ChIP). ChIP has been widely used to map the localization of post-translationally modified histones or histone variants on the genome or on a specific gene locus, or to map the association of transcription factors or chromatin modifying enzymes to the genome. In spite of its power, ChIP is a cumbersome procedure and typically requires large numbers of cells. This review outlines variations elaborated on the ChIP assay to shorten the procedure, make it suitable for small cell numbers and unravel the multiplicity of histone modifications on a single locus. In addition, the combination of ChIP assays with DNA microarray and high-throughput sequencing technologies has in recent years enabled the profiling of histone modifications and transcription factor occupancy sites throughout the genome and in a high-resolution manner throughout a genomic region of interest. We also review applications of ChIP to the mapping of histone modifications or transcription factor binding at the genome-wide level. Finally, we speculate on future perspectives opened by the combination of emerging ChIP-related technologies.