An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

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

Abstract

We describe Cleavage Under Targets and Release Using Nuclease (CUT&RUN), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. Unlike Chromatin Immunoprecipitation (ChIP), which fragments and solubilizes total chromatin, CUT&RUN is performed in situ, allowing for both quantitative high-resolution chromatin mapping and probing of the local chromatin environment. When applied to yeast and human nuclei, CUT&RUN yielded precise transcription factor profiles while avoiding cross-linking and solubilization issues. CUT&RUN is simple to perform and is inherently robust, with extremely low backgrounds requiring only ~1/10th the sequencing depth as ChIP, making CUT&RUN especially cost-effective for transcription factor and chromatin profiling. When used in conjunction with native ChIP-seq and applied to human CTCF, CUT&RUN mapped long range contacts at high resolution. We conclude that in situ mapping of protein-DNA interactions by CUT&RUN is an attractive alternative to ChIP-seq.

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The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Peter J Skene

    Basic Sciences Division, Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7621-8685
  2. Steven Henikoff

    Basic Sciences Division, Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, United States
    For correspondence
    steveh@fhcrc.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7621-8685

Funding

Howard Hughes Medical Institute (Henikoff)

  • Peter J Skene

Howard Hughes Medical Institute (Henikoff)

  • Steven Henikoff

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Danny Reinberg, Howard Hughes Medical Institute, New York University School of Medicine, United States

Version history

  1. Received: September 26, 2016
  2. Accepted: January 6, 2017
  3. Accepted Manuscript published: January 12, 2017 (version 1)
  4. Accepted Manuscript updated: January 16, 2017 (version 2)
  5. Version of Record published: February 15, 2017 (version 3)

Copyright

© 2017, 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
(2017)
An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites
eLife 6:e21856.
https://doi.org/10.7554/eLife.21856

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https://doi.org/10.7554/eLife.21856

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