Rxivist logo

Improved CUT&RUN chromatin profiling and analysis tools

By Michael P. Meers, Terri Bryson, Steven Henikoff

Posted 06 Mar 2019
bioRxiv DOI: 10.1101/569129

We previously described a novel alternative to Chromatin Immunoprecipitation, Cleavage Under Targets & Release Using Nuclease (CUT&RUN), in which unfixed permeabilized cells are incubated with antibody, followed by binding of a Protein A-Micrococcal Nuclease (pA/MNase) fusion protein ([1][1]). Upon activation of tethered MNase, the bound complex is excised and released into the supernatant for DNA extraction and sequencing. Here we introduce four enhancements to CUT&RUN: 1) a hybrid Protein A-Protein G-MNase construct that expands antibody compatibility and simplifies purification; 2) a modified digestion protocol that inhibits premature release of the nuclease-bound complex; 3) a calibration strategy based on carry-over of E. coli DNA introduced with the fusion protein; and 4) a novel peak-calling strategy customized for the low-background profiles obtained using CUT&RUN. These new features, coupled with the previously described low-cost, high efficiency, high reproducibility and high-throughput capability of CUT&RUN make it the method of choice for routine epigenomic profiling. [1]: #ref-1

Download data

  • Downloaded 12,124 times
  • Download rankings, all-time:
    • Site-wide: 571
    • In molecular biology: 11
  • Year to date:
    • Site-wide: 2,236
  • Since beginning of last month:
    • Site-wide: 2,236

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)