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Cleavage under targets and release using nuclease (CUT&RUN) is an epigenomic profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein–DNA complexes into the supernatant for paired-end DNA sequencing. CUT&RUN can be performed on the bench-top in a day from live cells to purified DNA, and has been adapted for full automation. As only the targeted fragments enter into solution, and the vast majority of DNA is left behind, CUT&RUN has exceptionally low background levels, which reduces sequencing costs. CUT&RUN provides near base-pair resolution, is free of solubility and DNA accessibility artifacts, and has been used to profile histone modifications and transcription factors in small samples and single cells. The method can be used to detect long-range 3D contacts without cross-linking and when used with salt fractionation CUT&RUN can profile chromatin features based on solubility. CUT&RUN supernatants have also been used as input for chromatin immunoprecipitation with sequencing to map specific components of chromatin complexes genome-wide.
Image source: Skene & Henikoff, ELife 2017 Figure 1A