title: An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites.
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 crosslinking 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 directional long range contact sites at high resolution. We conclude that in situ mapping of protein-DNA interactions by CUT&RUN is an attractive alternative to ChIP-seq.
authors.affiliation: Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Skene
authors.affiliation: Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.
authors.forename: Steven
authors.identifier: 0000-0002-7621-8685
authors.initials: S
authors.lastname: Henikoff
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D006801:Humans; D008836:Micrococcal Nuclease / Q000378:metabolism; D008967:Molecular Biology / Q000379:methods*; D011485:Protein Binding; D012441:Saccharomyces cerevisiae; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA; D008836:Micrococcal Nuclease
keywords: DNA sequencing; S. cerevisiae; chromatin; chromosomes; genes; human; in situ profiling; transcription factors