CUT&Tag for efficient epigenomic profiling of small samples and single cells

Nat Commun. 2019 Apr 29;10(1):1930. doi: 10.1038/s41467-019-09982-5.

Abstract

Many chromatin features play critical roles in regulating gene expression. A complete understanding of gene regulation will require the mapping of specific chromatin features in small samples of cells at high resolution. Here we describe Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components. In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a protein A-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background. All steps from live cells to sequencing-ready libraries can be performed in a single tube on the benchtop or a microwell in a high-throughput pipeline, and the entire procedure can be performed in one day. We demonstrate the utility of CUT&Tag by profiling histone modifications, RNA Polymerase II and transcription factors on low cell numbers and single cells.

Publication types

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

MeSH terms

  • Chromatin / chemistry*
  • Chromatin / metabolism
  • Epigenomics / methods*
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation
  • Genomic Library
  • High-Throughput Nucleotide Sequencing
  • Histone Code
  • Histones / genetics
  • Histones / metabolism
  • Humans
  • K562 Cells
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Single-Cell Analysis / methods*
  • Staining and Labeling / methods*
  • Staphylococcal Protein A / genetics
  • Staphylococcal Protein A / metabolism
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transposases / genetics
  • Transposases / metabolism

Substances

  • Chromatin
  • Histones
  • Recombinant Fusion Proteins
  • Staphylococcal Protein A
  • Tn5 transposase
  • Transcription Factors
  • RNA Polymerase II
  • Transposases