TY - JOUR TI - An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites AU - Skene, Peter J AU - Henikoff, Steven A2 - Reinberg, Danny VL - 6 PY - 2017 DA - 2017/01/12 SP - e21856 C1 - eLife 2017;6:e21856 DO - 10.7554/eLife.21856 UR - https://doi.org/10.7554/eLife.21856 AB - 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. KW - transcription factors KW - chromatin KW - in situ profiling KW - DNA sequencing JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -