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

  1. Peter J Skene
  2. Steven Henikoff  Is a corresponding author
  1. Fred Hutchinson Cancer Research Center, United States

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.

Article and author information

Author details

  1. Peter J Skene

    N/A, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. 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.

Reviewing Editor

  1. Joaquín M Espinosa, University of Colorado at Boulder, United States

Publication history

  1. Received: June 4, 2015
  2. Accepted: June 9, 2015
  3. Accepted Manuscript published: June 16, 2015 (version 1)
  4. Version of Record published: June 25, 2015 (version 2)

Copyright

© 2015, Skene & Henikoff

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Peter J Skene
  2. Steven Henikoff
(2015)
A simple method for generating high-resolution maps of genome wide protein binding
eLife 4:e09225.
https://doi.org/10.7554/eLife.09225

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