title: The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision.
abstract: Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA interactions. ChIP coupled to high throughput sequencing (ChIP-seq) is commonly used to determine the genomic location of proteins that interact with chromatin. However, ChIP-seq is hampered by relatively low mapping resolution of several hundred base pairs and high background signal. The ChIP-exo method is a refined version of ChIP-seq that substantially improves upon both resolution and noise. The key distinction of the ChIP-exo methodology is the incorporation of lambda exonuclease digestion in the library preparation workflow to effectively footprint the left and right 5' DNA borders of the protein-DNA crosslink site. The ChIP-exo libraries are then subjected to high throughput sequencing. The resulting data can be leveraged to provide unique and ultra-high resolution insights into the functional organization of the genome. Here, we describe the ChIP-exo method that we have optimized and streamlined for mammalian systems and next-generation sequencing-by-synthesis platform.
authors.affiliation: Department of Molecular Physiology and Biophysics, Vanderbilt University.
authors.forename: Andrea A
authors.initials: AA
authors.lastname: Perreault
authors.affiliation: Department of Molecular Physiology and Biophysics, Vanderbilt University; bryan.venters@vanderbilt.edu.
authors.forename: Bryan J
authors.initials: BJ
authors.lastname: Venters
mesh_terms: D000818:Animals; D020029:Base Pairing; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D059014:High-Throughput Nucleotide Sequencing
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA