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

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.

Automated summary

This study presents a single-cell DNA methylation sequencing method that can accurately resolve the DNA methylation profiles of individual cells. The sciEM method improves sequencing alignment rates, reduces adapter contamination, and over-estimation of DNA methylation levels. The researchers successfully applied this method to resolve single-cell DNA methylation of major cell types in the human brain.