Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression

Nat Biotechnol. 2021 Jul;39(7):819-824. doi: 10.1038/s41587-021-00865-z. Epub 2021 Apr 12.


Methods for quantifying gene expression1 and chromatin accessibility2 in single cells are well established, but single-cell analysis of chromatin regions with specific histone modifications has been technically challenging. In this study, we adapted the CUT&Tag method3 to scalable nanowell and droplet-based single-cell platforms to profile chromatin landscapes in single cells (scCUT&Tag) from complex tissues and during the differentiation of human embryonic stem cells. We focused on profiling polycomb group (PcG) silenced regions marked by histone H3 Lys27 trimethylation (H3K27me3) in single cells as an orthogonal approach to chromatin accessibility for identifying cell states. We show that scCUT&Tag profiling of H3K27me3 distinguishes cell types in human blood and allows the generation of cell-type-specific PcG landscapes from heterogeneous tissues. Furthermore, we used scCUT&Tag to profile H3K27me3 in a patient with a brain tumor before and after treatment, identifying cell types in the tumor microenvironment and heterogeneity in PcG activity in the primary sample and after treatment.

Publication types

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

MeSH terms

  • Brain Neoplasms / genetics
  • Brain Neoplasms / metabolism
  • Cell Differentiation
  • Chromatin / genetics
  • Chromatin / physiology*
  • Embryonic Stem Cells
  • Gene Expression Regulation
  • Gene Silencing
  • Humans
  • Jumonji Domain-Containing Histone Demethylases / genetics
  • Jumonji Domain-Containing Histone Demethylases / metabolism
  • K562 Cells
  • Polycomb-Group Proteins / genetics
  • Polycomb-Group Proteins / metabolism*
  • Single-Cell Analysis*


  • Chromatin
  • Polycomb-Group Proteins
  • Jumonji Domain-Containing Histone Demethylases