Single-cell DNA methylation sequencing by combinatorial indexing and enzymatic DNA methylation conversion
Zac Chatterton, Praves Lamichhane, Diba Ahmadi Rastegar, Lauren Fitzpatrick, Hélène Lebhar, Christopher P. Marquis, Glenda M. Halliday, John B. Kwok
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: > 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.