Chromatin immunoprecipitation, or ChIP, is established in epigenetic research as a powerful method for investigating genome-wide DNA-protein interactions in the cell, aiding researchers in understanding chromatin dynamics and epigenetic mechanisms. With the recent technological advancement of next generation sequencing, the ChIP assay can be combined with the power of massively parallel sequencing platforms like Illumina to map the exact binding sites across the entire genome to which the protein of interest is bound.
Prior to ChIP-seq, ChIP-on-ChIP or ChIP-chip was the popular method but has since been replaced as the method of choice. ChIP-chip combines chromatin immunoprecipitation with DNA microarrays and offers a global view of where the protein binds to the DNA. The protocol for ChIP-chip and ChIP-Seq are the same until the last step: crosslink, sonicate, immunoprecipitate, reverse crosslink, and lastly, microarray (for ChIP-chip) or sequence the DNA fragments (for ChIP-seq). But unlike ChIP-seq, ChIP-chip cannot provide actual DNA sequences of precipitated fragments and you cannot increase sensitivity as you can in ChIP-seq by simply increasing the number of counts.
ChIP-seq overcomes many of the limitations of other assays used for studying protein-DNA interactions and allows investigators to pinpoint a specific gene sequence that a specific protein of interest binds to, for instance, a target sequence of a transcription factor. This has helped epigenetic researchers advance their studies and conduct more targeted investigation into protein-DNA interactions and especially offers new insight into disease development.