Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq)

Nat Commun. 2019 Aug 20;10(1):3747. doi: 10.1038/s41467-019-11559-1.

Abstract

Modern next-generation sequencing-based methods have empowered researchers to assay the epigenetic states of individual cells. Existing techniques for profiling epigenetic marks in single cells often require the use and optimization of time-intensive procedures such as drop fluidics, chromatin fragmentation, and end repair. Here we describe ACT-seq, a streamlined method for mapping genome-wide distributions of histone tail modifications, histone variants, and chromatin-binding proteins in a small number of or single cells. ACT-seq utilizes a fusion of Tn5 transposase to Protein A that is targeted to chromatin by a specific antibody, allowing chromatin fragmentation and sequence tag insertion specifically at genomic sites presenting the relevant antigen. The Tn5 transposase enables the use of an index multiplexing strategy (iACT-seq), which enables construction of thousands of single-cell libraries in one day by a single researcher without the need for drop-based fluidics or visual sorting. We conclude that ACT-seq present an attractive alternative to existing techniques for mapping epigenetic marks in single cells.

Publication types

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

MeSH terms

  • Antibodies / immunology
  • Antibodies / metabolism
  • Chromatin / immunology
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation
  • Chromosome Mapping / methods*
  • Epigenomics / methods
  • HEK293 Cells
  • Histone Code*
  • Histones / genetics*
  • Histones / metabolism
  • Humans
  • Protein Processing, Post-Translational
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Sequence Analysis, DNA / methods
  • Single-Cell Analysis / methods*
  • Staining and Labeling / methods
  • Staphylococcal Protein A / genetics
  • Staphylococcal Protein A / metabolism
  • Transposases / genetics
  • Transposases / metabolism

Substances

  • Antibodies
  • Chromatin
  • Histones
  • Recombinant Fusion Proteins
  • Staphylococcal Protein A
  • Tn5 transposase
  • Transposases