Concomitant sequencing of accessible chromatin and mitochondrial genomes in single cells using mtscATAC-seq

Item Type:	Article
Title:	Concomitant sequencing of accessible chromatin and mitochondrial genomes in single cells using mtscATAC-seq
Creators Name:	Ludwig, L.S. and Lareau, C.A.
Abstract:	Mitochondria are unique organelles of eukaryotic cells that carry their own multicopy number and circular genome. In most mammals, including humans and mice, the size of the chromosome is ~16,000 base pairs and unlike nuclear DNA, mitochondrial DNA (mtDNA) is not densely compacted. This results in mtDNA to be highly accessible for enzymes such as the Tn5 transposase, commonly used for accessible chromatin profiling of nuclear chromatinized DNA. Here, we describe a method for the concomitant sequencing of mtDNA and accessible chromatin in thousands of individual cells via the mitochondrial single-cell assay for transposase accessible chromatin by sequencing (mtscATAC-seq). Our approach extends the utility of existing scATAC-seq products and protocols as we (Nam et al, Nat Rev Genet 22:3-18, 2021) fix cells using formaldehyde to retain mitochondria and its mtDNA within its originating cell, (Buenrostro et al, Nat Methods 10:1213-1218, 2013) modify lysis conditions to permeabilize cells and mitochondria, and (Corces et al, Nat Methods 14:959-962, 2017) optimize bioinformatic processing protocols to collectively increase mitochondrial genome coverage for downstream analysis. Here, we discuss the essentials for the experimental and computational methodologies to generate and analyze thousands of multiomic profiles of single cells over the course of a few days, enabling the profiling of accessible chromatin and mtDNA genotypes to reconstruct clonal relationships and studies of mitochondrial genetics and disease.
Keywords:	Single Cell Multiomics, Accessible Chromatin Profiling, Mitochondrial DNA, Somatic Mutation, Lineage Tracing, Pathogenic Mutation, Mitochondrial Disease, Animals, Mice
Source:	Methods in Molecular Biology
Series Name:	Methods in Molecular Biology
Title of Book:	Chromatin Accessibility
ISSN:	1064-3745
ISBN:	978-1-0716-2898-0
Publisher:	Springer / Humana Press
Volume:	2611
Page Range:	269-282
Date:	2023
Official Publication:	https://doi.org/10.1007/978-1-0716-2899-7_14
PubMed:	View item in PubMed

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