Virtually all aspects of cellular function, such as replication of DNA, separation of
chromosomes during cell division, DNA repair, or gene expression, depend on the
interaction of proteins with DNA. The nature of DNA-binding proteins is wide and
ranges from structural proteins making up the nucleosome, enzymes modulating
chromatin structure to enable, facilitate, or repress gene expression, transcription
factors, and various cofactors. The biological significance of these associations in the
context of gene expression, development, cell differentiation, and disease has immen￾sely been enhanced in the past 20 years by the advent of a technique referred to as
chromatin immunoprecipitation, or ChIP. The purpose of the ChIP assay is to identify
genomic sequence(s) associated with a protein of interest, for example, your favorite
transcription factor, in the genome. ChIP, then, has become the technique of choice to
determine the genomic enrichment profiles of transcription factors, post-translationally
modified histones, histone variants, or chromatin-modifying enzymes. In the ChIP
assay, the protein of interest is immunoprecipitated from a chromatin preparation using
specific antibodies. After stringent washes, the DNA is released and the sequences
bound by the immunoprecipitated protein are identified. Sequence identification
methods have rapidly evolved from dot- or slot-blots in the early days to polymerase
chain reaction. Subsequently, the combination of ChIP with DNA microarray or high￾throughput sequencing technologies has enabled the profiling of protein occupancy on
a genome-wide scale. It has also promoted the appearance of new algorithms for
mapping protein binding throughout the genome.