An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites
- 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.
Data availability
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Cut-and-Run in situ factor profiling maps DNA binding and 3D contact sites at high resolutionPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE84474).
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High-resolution mapping of transcription factor binding sites on native chromatin.Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE45672).
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CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for TranscriptionPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE72816).
Article and author information
Author details
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
© 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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An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites
eLife 6:e21856.
https://doi.org/10.7554/eLife.21856
Further reading
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- Chromosomes and Gene Expression
A new technique called CUT&RUN can map the distribution of proteins on the genome with higher resolution and accuracy than existing approaches.
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- Chromosomes and Gene Expression
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