PT  - JOURNAL ARTICLE
AU  - Skene, Peter J.
AU  - Henikoff, Steven
TI  - CUT&RUN: Targeted <em>in situ</em> genome-wide profiling with high efficiency for low cell numbers
AID  - 10.1101/193219
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 193219
4099  - http://biorxiv.org/content/early/2017/09/24/193219.short
4100  - http://biorxiv.org/content/early/2017/09/24/193219.full
AB  - 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. As only the targeted fragments enter into solution, and the vast majority of DNA is left behind, CUT&RUN has exceptionally low background levels. CUT&RUN outperforms the most widely-used Chromatin Immunoprecipitation (ChIP) protocols in resolution, signal-to-noise, and depth of sequencing required. In contrast to ChIP, CUT&RUN is free of solubility and DNA accessibility artifacts and can be used to profile insoluble chromatin and to detect long-range 3D contacts without cross-linking. Here we present an improved CUT&RUN protocol that does not require isolation of nuclei and provides high-quality data starting with only 100 cells for a histone modification and 1000 cells for a transcription factor. From cells to purified DNA CUT&RUN requires less than a day at the lab bench.