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

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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.

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Peter J Skene

N/A, Fred Hutchinson Cancer Research Center, Seattle, United States

Competing interests
The authors declare that no competing interests exist.
Steven Henikoff

N/A, Fred Hutchinson Cancer Research Center, Seattle, United States

For correspondence
steveh@fhcrc.org

Competing interests
The authors declare that no competing interests exist.

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