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

ABSTRACT:

Background

DNA 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.

Results

The 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.

Conclusion

To our knowledge sciEM represents the first non-bisulfite single-cell DNA methylation sequencing approach with single-base resolution.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13578-022-00938-9.

SUBMITTER: Chatterton Z

PROVIDER: S-EPMC9811750 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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