title: Precise Identification of DNA-Binding Proteins Genomic Location by Exonuclease Coupled Chromatin Immunoprecipitation (ChIP-exo).
abstract: DNA-binding proteins play a crucial role in all living organisms by interacting with various DNA sequences across the genome. While several methods have been used to study the interaction between DNA and proteins in vitro, chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become the standard technique for identifying the genome-wide location of DNA-binding proteins in vivo. However, the resolution of standard ChIP-seq methodology is limited by the DNA fragmentation process and presence of contaminating DNA. A significant improvement of the ChIP-seq technique results from the addition of an exonuclease treatment during the immunoprecipitation step (ChIP-exo) that lowers background noise and more importantly increases the identification of binding sites to a level near to single-base resolution by effectively footprinting DNA-bound proteins. By doing so, ChIP-exo offers new opportunities for a better characterization of the complex and fascinating architecture that resides in DNA-proteins interactions and provides new insights for the comprehension of important molecular mechanisms.
authors.affiliation: Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, QC, Canada, J1K 2R1.
authors.forename: Dominick
authors.initials: D
authors.lastname: Matteau
authors.affiliation: Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, QC, Canada, J1K 2R1. sebastien.rodrigue@usherbrooke.ca.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Rodrigue
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D053938:DNA Fragmentation; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics; D005092:Exonucleases / Q000737:chemistry* / Q000235:genetics; D016678:Genome; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors; D005092:Exonucleases
keywords: ChIP-exo; Chromatin immunoprecipitation; DNA footprinting; DNA-binding protein; Exonuclease degradation; Formaldehyde cross-linking; Gene regulation; Genomics; Next-generation sequencing; Protein-DNA interaction