A simple method for generating high-resolution maps of genome-wide protein binding

• Main Authors: Peter J Skene, Steven Henikoff
• Format: Article
• Language: English
• Published: eLife Sciences Publications Ltd 2015-06-01
• Series: eLife
• Subjects: transcription factor; RNA polymerase II; CTCF
• Online Access: https://elifesciences.org/articles/09225

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.