Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs

Epigenetics Chromatin. 2018 Dec 21;11(1):74. doi: 10.1186/s13072-018-0243-8.


Background: Our understanding of eukaryotic gene regulation is limited by the complexity of protein-DNA interactions that comprise the chromatin landscape and by inefficient methods for characterizing these interactions. We recently introduced CUT&RUN, an antibody-targeted nuclease cleavage method that profiles DNA-binding proteins, histones and chromatin-modifying proteins in situ with exceptional sensitivity and resolution.

Results: Here, we describe an automated CUT&RUN platform and apply it to characterize the chromatin landscapes of human cells. We find that automated CUT&RUN profiles of histone modifications crisply demarcate active and repressed chromatin regions, and we develop a continuous metric to identify cell-type-specific promoter and enhancer activities. We test the ability of automated CUT&RUN to profile frozen tumor samples and find that our method readily distinguishes two pediatric glioma xenografts by their subtype-specific gene expression programs.

Conclusions: The easy, cost-effective workflow makes automated CUT&RUN an attractive tool for high-throughput characterization of cell types and patient samples.

Keywords: CUT&RUN; Chromatin regulators; Histone modifications; Transcription factors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Chromatin / genetics
  • Chromatin Immunoprecipitation / methods*
  • DNA-Binding Proteins / analysis
  • DNA-Binding Proteins / classification
  • DNA-Binding Proteins / genetics
  • Enhancer Elements, Genetic / genetics
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Neoplastic / genetics
  • High-Throughput Screening Assays / methods
  • Histone Code / genetics
  • Histones / genetics
  • Humans
  • In Situ Hybridization / methods
  • K562 Cells
  • Promoter Regions, Genetic / genetics
  • Protein Binding / genetics
  • Software
  • Transcription Factors / genetics


  • Chromatin
  • DNA-Binding Proteins
  • Histones
  • Transcription Factors