ABSTRACT
Traditional methods such as electrophoresis gel mobility shi and DNase I footprinting assays have successfully identied TF binding sites and specic DNA-associated protein modications and their roles in regulating specic genes, but these experiments are limited in scale and resolution. is limited utility has sparked the development of chromatin immunoprecipitation with DNA microarray (ChIP-chip) to identify interactions between proteins and DNA in larger scales. However, with the advent of lower cost and higher speed next-generation DNA sequencing technologies, ChIP-seq is gradually replacing ChIP-chip as the tour de force for the detection of DNA-binding proteins on a genome-wide basis. e ChIP-seq technique usually involves xing intact cells with formaldehyde, a reversible protein-DNA cross-linking agent that serves to x or preserve the protein-DNA interactions occurring in the cell. e cells are then lysed and chromatin fragments are isolated from the nuclei by sonication or nuclease digestion. is is followed by the selective immunoprecipitation of protein-DNA complexes by utilizing specic protein antibodies and their conjugated beads. e cross-links are then reversed, and the immunoprecipitated and released DNA is subjected to next-generation DNA sequencing before the specic binding sites of the probed protein are identied by a computation analysis.
