Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility

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Item Type:	Article
Title:	Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility
Creators Name:	Lareau, C.A., Liu, V., Muus, C., Praktiknjo, S.D., Nitsch, L., Kautz, P., Sandor, K., Yin, Y., Gutierrez, J.C., Pelka, K., Satpathy, A.T., Regev, A., Sankaran, V.G. and Ludwig, L.S.
Abstract:	Natural sequence variation within mitochondrial DNA (mtDNA) contributes to human phenotypes and may serve as natural genetic markers in human cells for clonal and lineage tracing. We recently developed a single-cell multi-omic approach, called 'mitochondrial single-cell assay for transposase-accessible chromatin with sequencing' (mtscATAC-seq), enabling concomitant high-throughput mtDNA genotyping and accessible chromatin profiling. Specifically, our technique allows the mitochondrial genome-wide inference of mtDNA variant heteroplasmy along with information on cell state and accessible chromatin variation in individual cells. Leveraging somatic mtDNA mutations, our method further enables inference of clonal relationships among native ex vivo-derived human cells not amenable to genetic engineering-based clonal tracing approaches. Here, we provide a step-by-step protocol for the use of mtscATAC-seq, including various cell-processing and flow cytometry workflows, by using primary hematopoietic cells, subsequent single-cell genomic library preparation and sequencing that collectively take ~3-4 days to complete. We discuss experimental and computational data quality control metrics and considerations for the extension to other mammalian tissues. Overall, mtscATAC-seq provides a broadly applicable platform to map clonal relationships between cells in human tissues, investigate fundamental aspects of mitochondrial genetics and enable additional modes of multi-omic discovery.
Keywords:	Chromatin Immunoprecipitation Sequencing, Chromatin, Mitochondrial DNA, Genotype, High-Throughput Nucleotide Sequencing, Multiomics, DNA Sequence Analysis, Animals, Mammals
Source:	Nature Protocols
ISSN:	1754-2189
Publisher:	Nature Publishing Group
Volume:	18
Number:	5
Page Range:	1416-1440
Date:	May 2023
Additional Information:	Copyright © 2023. Springer Nature Limited.
Official Publication:	https://doi.org/10.1038/s41596-022-00795-3
External Fulltext:	View full text on PubMed Central
PubMed:	View item in PubMed

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