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

Abstract
Data availability
Article and author information
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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 ~1/10^th 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.

Data availability

The following data sets were generated

1. Skene PJ
2. Henikoff S
(2016) Cut-and-Run in situ factor profiling maps DNA binding and 3D contact sites at high resolution
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE84474).

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=ynsngiuiplovjut&acc=GSE84474

The following previously published data sets were used

(2014) High-resolution mapping of transcription factor binding sites on native chromatin.
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE45672).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45672
1. Luo OJ
2. Tang Z
3. Li X
4. Ruan Y
(2015) CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE72816).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72816

Article and author information

Author details

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.

"This ORCID iD identifies the author of this article:" 0000-0002-7621-8685
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.

"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.

Copyright

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.