1. Chromosomes and Gene Expression

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
https://doi.org/10.7554/eLife.09225
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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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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

Version 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

Share this article

https://doi.org/10.7554/eLife.09225

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