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 Marquis; Glenda Halliday; John B Kwok

doi:10.1186/s13578-022-00938-9

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

Cell Biosci. 2023 Jan 4;13(1):2. doi: 10.1186/s13578-022-00938-9.

Authors

Zac Chatterton^{1

2}, Praves Lamichhane^{3

4}, Diba Ahmadi Rastegar^{3

4}, Lauren Fitzpatrick^{3

4}, Hélène Lebhar⁵, Christopher Marquis⁶, Glenda Halliday^{3

4}, John B Kwok^{3

4}

Affiliations

¹ Brain and Mind Centre, The University of Sydney, Camperdown, Australia. zac.chatterton@sydney.edu.au.
² School of Medical Science, The University of Sydney, Camperdown, Australia. zac.chatterton@sydney.edu.au.
³ Brain and Mind Centre, The University of Sydney, Camperdown, Australia.
⁴ School of Medical Science, The University of Sydney, Camperdown, Australia.
⁵ Recombinant Products Facility, University of New South Wales, Kensington, Australia.
⁶ School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Australia.

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.

Keywords: APOBEC; Brain; DNA methylation; Epigenetics; Single-cell.