ChIP-exo Protocol [Download]
Mechanisms of protein-DNA interactions inside of the nucleus of the cell have been intensely investigated over the past several decades. Chromatin immunoprecipitation (ChIP) is the most widely used method to identify genomic locations of DNA-binding proteins. The major limitation of the ChIP method is the necessity of shearing chromatin, which generates heterogeneously sized long DNA fragments that produce imprecision in mapping. Moreover, ChIP creates erroneous binding locations from non-specific background DNA, which results in a high uncertainty of DNA-binding sites in the genome. To overcome these problems, Ho-Sung developed a novel genomic mapping method, called ChIP-exo, during his Ph.D. studies in the Frank Pugh's lab. This method allows us to detect precise protein-DNA interactions by combining ChIP with exonuclease digestion.
wikipedia
ChIP-exo gives extremely high resolution with single nucleotide mapping accuracy and removes nearly all contaminating DNA. This method was published in a book chapter, patented, and commercialized by biotechnological companies, seeking to maximize its influence on the scientific community. ChIP-exo has revolutionized our understanding of gene regulation by providing unprecedented high-definition views of protein complexes bound to DNA. This method has been replacing the current ChIP method and is being increasingly adopted by many researchers in science. This contribution is evidenced by the more than 460 citations of the paper in Cell since 2012.
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