High-Resolution Chromatin Profiling Using CUT&RUN

Curr Protoc Mol Biol. 2019 Apr;126(1):e85. doi: 10.1002/cpmb.85. Epub 2019 Jan 28.


Determining the genomic location of DNA-binding proteins is essential to understanding their function. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a powerful method for mapping protein-DNA interactions at high resolution. In CUT&RUN, a recombinant protein A-microccocal nuclease (pA-MN) fusion is recruited by an antibody targeting the chromatin protein of interest; this can be done with either uncrosslinked or formaldehyde-crosslinked cells. DNA fragments near sites of antibody binding are released from the insoluble bulk chromatin through endonucleolytic cleavage and used to build barcoded DNA-sequencing libraries that can be sequenced in pools of at least 30. Therefore, CUT&RUN provides an alternative to ChIP-seq approaches for mapping chromatin proteins, which typically have relatively high signal-to-noise ratios, while using fewer cells and at a lower cost. Here, we describe the methods for performing CUT&RUN, generating DNA-sequencing libraries, and analyzing the resulting datasets. © 2019 by John Wiley & Sons, Inc.

Keywords: CUT&RUN; chromatin; protein A-micrococcal nuclease; transcription factor.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Binding Sites
  • Chromatin / chemistry*
  • DNA / metabolism
  • DNA-Binding Proteins / analysis*
  • Molecular Biology / methods*
  • Protein Binding


  • Chromatin
  • DNA-Binding Proteins
  • DNA