Chromatin Immunoprecipitation (ChIP) is a method used to detect DNA-protein interactions in vivo. ChIP has been widely applied to assess the abundance of various epigenetic regulators, including modified histones, in various regions of cellular and viral chromatin. During the procedure, DNA binding proteins are covalently cross-linked to DNA, and the isolated chromatin is broken into pieces of 300-500 bps in length on average. Thereafter, using specific antibody directed against the protein of interest the covalently cross-linked DNA is pulled down together with Protein A or G carrying beads that bind the Fc fragment of the antibody. After the reversal of crosslinks and DNA isolation, one may analyze the precipitated DNA fragments by quantitative and qualitative methods to assess the relative abundance of the examined protein in a region or within the genome studied in vivo. In addition to the analysis of transcription factor binding, ChIP has proved to be a reliable method to map histone modifications across cellular and viral epigenomes.
Keywords: Chromatin; Epigenetics; In vivo; Protein-DNA interaction.