Efficient low-cost chromatin profiling with CUT&Tag

Nat Protoc. 2020 Oct;15(10):3264-3283. doi: 10.1038/s41596-020-0373-x. Epub 2020 Sep 10.


We recently introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in permeabilized nuclei. These antibodies are then used to tether the cut-and-paste transposase Tn5. Activation of the transposase simultaneously cleaves DNA and adds adapters ('tagmentation') for paired-end DNA sequencing. Here, we introduce a streamlined CUT&Tag protocol that suppresses DNA accessibility artefacts to ensure high-fidelity mapping of the antibody-targeted protein and improves the signal-to-noise ratio over current chromatin profiling methods. Streamlined CUT&Tag can be performed in a single PCR tube, from cells to amplified libraries, providing low-cost genome-wide chromatin maps. By simplifying library preparation CUT&Tag requires less than a day at the bench, from live cells to sequencing-ready barcoded libraries. As a result of low background levels, barcoded and pooled CUT&Tag libraries can be sequenced for as little as $25 per sample. This enables routine genome-wide profiling of chromatin proteins and modifications and requires no special skills or equipment.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Chromatin / genetics*
  • Chromosome Mapping / methods*
  • DNA / genetics
  • Epigenomics / methods*
  • Gene Library
  • High-Throughput Nucleotide Sequencing / methods
  • Histones / metabolism
  • Sequence Analysis, DNA / methods
  • Single-Cell Analysis / methods
  • Transposases / genetics
  • Transposases / metabolism


  • Chromatin
  • Histones
  • Tn5 transposase
  • DNA
  • Transposases