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Dual detection of chromatin accessibility and DNA methylation using ATAC-Me

Nature Protocols volume 16, pages 5377–5397 (2021)Cite this article

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Abstract

The epigenome is multidimensional, with individual molecular components operating on different levels to control transcriptional output. Techniques that combine measurements of these features can reveal their precise correspondence in genomic space, or temporal connectivity, to better understand how they jointly regulate genes. ATAC-Me is an integrated method to probe DNA methylation and chromatin accessibility from a single DNA fragment library. Intact nuclei undergo Tn5 transposition to isolate DNA fragments within nucleosome-free regions. Isolated fragments are exposed to sodium bisulfite before library amplification and sequencing. A typical ATAC-Me experiment detects ~60,000–75,000 peak regions (P < 0.05), covering ~3–4 million CpG sites with at least 5× coverage. These sites display a range of methylation values depending on the cellular and genomic context. The approach is well suited for time course studies that aim to capture chromatin and DNA methylation dynamics in tandem during cellular differentiation. The protocol is completed in 2 d with standard molecular biology equipment and expertise. Analysis of resulting data uses publicly available software requiring basic bioinformatics skills to interpret results.

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Fig. 1: General workflow for the ATAC-Me protocol.
Fig. 2: Fragment distribution at quality check steps.
Fig. 3: Assessing library complexity versus data quality.
Fig. 4: Data analysis pipeline and peak caller characteristics.
Fig. 5: Anticipated results and ATAC-Me data visualization.

Data availability

Data used in this protocol have been deposited in the Gene Expression Omnibus database with accession number GSE166267. Figure 5 is derived from the raw data.

Code availability

Bioinformatic pipelines described in this protocol have been made available in GitHub (https://github.com/HodgesGenomicsLab/NatProtocols_ATACme)51.

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Acknowledgements

We thank VANTAGE for their advice in sequencing the libraries. We thank members of the Hodges lab for helpful discussions. We thank the Kariolich and Gama labs for cell lines. This work was supported by National Institutes of Health (K22 CA184308 to E.H., T32HD007502 to K.B).

Author information

Author notes

  1. Kelly R. Barnett

    Present address: Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, USA

Authors and Affiliations

  1. Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA

    Lindsey N. Guerin, Kelly R. Barnett & Emily Hodges

  2. Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA

    Lindsey N. Guerin, Kelly R. Barnett & Emily Hodges

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  1. Lindsey N. Guerin
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Contributions

E.H. directed the project. L.G. and K.B. performed the experiments. L.G. and E.H wrote the manuscript.

Corresponding author

Correspondence to Emily Hodges.

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The authors declare no competing interests.

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Peer review information Nature Protocols thanks Suhn Kyong Rhie and Jörn Walter for their contribution to the peer review of this work.

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Key reference using this protocol

Barnett, K. et al. Mol. Cell 77, 1350–1364 e1356 (2020): https://doi.org/10.1016/j.molcel.2020.01.004 (2020)

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Guerin, L.N., Barnett, K.R. & Hodges, E. Dual detection of chromatin accessibility and DNA methylation using ATAC-Me. Nat Protoc 16, 5377–5397 (2021). https://doi.org/10.1038/s41596-021-00608-z

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