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

• Published in: Nature communications Vol. 10; no. 1; p. 3747
• Main Authors: Carter, Benjamin, Ku, Wai Lim, Kang, Jee Youn, Hu, Gangqing, Perrie, Jonathan, Tang, Qingsong, Zhao, Keji
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 20.08.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 45/15; 631/1647/2217; 631/337/100/2285; 631/337/100/2286; 631/337/176; Antibodies; Antibodies - immunology; Antibodies - metabolism; Antigens; Cell fusion; Cell number; Chromatin; Chromatin - immunology; Chromatin - metabolism; Chromatin Immunoprecipitation; Chromosome Mapping - methods; Epigenetics; Epigenomics - methods; Fluidics; Fragmentation; Gene mapping; HEK293 Cells; Histone Code; Histones; Histones - genetics; Histones - metabolism; Humanities and Social Sciences; Humans; multidisciplinary; Multiplexing; Next-generation sequencing; Optimization; Peptide mapping; Protein A; Protein Processing, Post-Translational; Proteins; Recombinant Fusion Proteins - genetics; Recombinant Fusion Proteins - metabolism; Science; Science (multidisciplinary); Sequence Analysis, DNA - methods; Sequences; Single-Cell Analysis - methods; Staining and Labeling - methods; Staphylococcal Protein A - genetics; Staphylococcal Protein A - metabolism; Transposase; Transposases - genetics; Transposases - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-11559-1

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. The authors introduce ACT-seq: a Tn5-based method for rapidly profiling epigenetic marks in bulk-cell and single-cell samples. ACT-seq avoids many laborious or time-consuming steps required for similar techniques including chromatin fragmentation and end repair.