Single-cell DNA methylation sequencing by combinatorial indexing and enzymatic DNA methylation conversion

Cell & Bioscience

Research

Zac Chatterton¹  Praves Lamichhane¹  Lauren Fitzpatrick¹  Glenda Halliday¹  Diba Ahmadi Rastegar¹  John B. Kwok¹  Hélène Lebhar²  Christopher Marquis³ 

[1] Brain and Mind Centre, The University of Sydney, Camperdown, Australia;School of Medical Science, The University of Sydney, Camperdown, Australia;Recombinant Products Facility, University of New South Wales, Kensington, Australia;School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Australia;

关键词: Epigenetics;    DNA methylation;    Single-cell;    Brain;    APOBEC;   

DOI  :  10.1186/s13578-022-00938-9

 received in 2022-10-12, accepted in 2022-12-07,  发布年份 2022

来源: Springer

【 摘 要 】

BackgroundDNA methylation is a critical molecular mark involved in cellular differentiation and cell-specific processes. Single-cell whole genome DNA methylation profiling methods hold great potential to resolve the DNA methylation profiles of individual cell-types. Here we present a method that couples single-cell combinatorial indexing (sci) with enzymatic conversion (sciEM) of unmethylated cytosines.ResultsThe sciEM method facilitates DNA methylation profiling of single-cells that is highly correlated with single-cell bisulfite-based workflows (r2 > 0.99) whilst improving sequencing alignment rates, reducing adapter contamination and over-estimation of DNA methylation levels (CpG and non-CpG). As proof-of-concept we perform sciEM analysis of the temporal lobe, motor cortex, hippocampus and cerebellum of the human brain to resolve single-cell DNA methylation of all major cell-types.ConclusionTo our knowledge sciEM represents the first non-bisulfite single-cell DNA methylation sequencing approach with single-base resolution.

【 授权许可】

CC BY   
© The Author(s) 2022

【 图 表 】

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