Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
- Fred Hutchinson Cancer Research Center, United States
Abstract
Chromatin accessibility mapping is a powerful approach to identify potential regulatory elements. A popular example is ATAC-seq, whereby Tn5 transposase inserts sequencing adapters into accessible DNA ('tagmentation'). CUT&Tag is a tagmentation-based epigenomic profiling method in which antibody tethering of Tn5 to a chromatin epitope of interest profiles specific chromatin features in small samples and single cells. Here we show that by simply modifying the tagmentation conditions for histone H3K4me2 or H3K4me3 CUT&Tag, antibody-tethered tagmentation of accessible DNA sites is redirected to produce chromatin accessibility maps that are indistinguishable from the best ATAC-seq maps. Thus, chromatin accessibility maps can be produced in parallel with CUT&Tag maps of other epitopes with all steps from nuclei to amplified sequencing-ready libraries performed in single PCR tubes in the laboratory or on a home workbench. As H3K4 methylation is produced by transcription at promoters and enhancers, our method identifies transcription-coupled accessible regulatory sites.
Data availability
Sequencing data have been deposited in GEO under accession code GSE158327
-
Efficient transcription-coupled chromatin accessibility mapping in situNCBI Gene Expression Omnibus, GSE158327.
-
CUT&Tag for efficient epigenomic profiling of small samples and single cellsNCBI Gene Expression Omnibus, GSE124557.
Article and author information
Author details
Funding
National Institutes of Health (R01 HG010492)
- Steven Henikoff
National Institutes of Health (R01 GM108699)
- Kami Ahmad
Chan Zuckerberg Initiative (Fred Hutch HCA Seed Network)
- Steven Henikoff
- Kami Ahmad
Howard Hughes Medical Institute (Henikoff)
- Steven Henikoff
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2020, Henikoff et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 16,003
- views
-
- 1,731
- downloads
-
- 110
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation
eLife 9:e63274.
https://doi.org/10.7554/eLife.63274
