title: A simple method for generating high-resolution maps of genome-wide protein binding.
abstract: Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution, and newer techniques require significant experimental alterations and complex bioinformatics. Previously, we have used a new crosslinking ChIP-seq protocol (X-ChIP-seq) to perform high-resolution mapping of RNA Polymerase II (Skene et al., 2014). Here, we build upon this work and compare X-ChIP-seq to existing methodologies. By using micrococcal nuclease, which has both endo- and exo-nuclease activity, to fragment the chromatin and thereby generate precise protein-DNA footprints, high-resolution X-ChIP-seq achieves single base-pair resolution of transcription factor binding. A significant advantage of this protocol is the minimal alteration to the conventional ChIP-seq workflow and simple bioinformatic processing.
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, United States.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Skene
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, United States.
authors.forename: Steven
authors.initials: S
authors.lastname: Henikoff
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D008836:Micrococcal Nuclease / Q000378:metabolism; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA; D008836:Micrococcal Nuclease
keywords: CTCF; D. melanogaster; RNA polymerase II; chromosomes; evolutionary biology; genes; genomics; human; transcription factors