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bioRxiv · 10.1101/2022.10.09.511389

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

Chatterton, Z.·Lamichhane, P.·Rastegar, D. A.·Fitzpatrick, L.·Lebhar, H.·Marquis, C.·Halliday, G.·Kwok, J.
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Abstract

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. The method facilitates single-base resolution 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.

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Chatterton, Z., Lamichhane, P., Rastegar, D. A., Fitzpatrick, L., Lebhar, H., Marquis, C., Halliday, G., Kwok, J.. 2022-10-09. Single-cell DNA methylation sequencing by combinatorial indexing and enzymatic DNA methylation conversion.. https://doi.org/10.1101/2022.10.09.511389

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