High-coverage allele-resolved single-cell DNA methylation profiling reveals cell lineage, X-inactivation state, and...

Area of Science:

• Epigenetics
• Genomics
• Cell Biology

Background:

• DNA methylation patterns in regulatory regions like enhancers and promoters are crucial for cell lineage and state.
• Current single-cell whole-genome bisulfite sequencing (scWGBS) methods have limitations in library efficiency and CpG coverage.
• These limitations hinder direct cell-to-cell comparisons and necessitate data summarization, obscuring regulatory element insights.

Purpose of the Study:

• To develop an improved scWGBS method for high-resolution single-cell DNA methylation profiling.
• To overcome the methodological and analytical shortcomings of existing scWGBS techniques.
• To enable detailed cell-to-cell comparisons and analysis of DNA methylation at individual regulatory elements.

Main Methods:

• Development and application of single-cell Deep and Efficient Epigenomic Profiling of methyl-C (scDEEP-mC).
• scDEEP-mC focuses on efficient generation of high-coverage DNA methylation libraries from single cells.
• Integration of methylation and copy-number data from scDEEP-mC.

Main Results:

• scDEEP-mC provides efficient, high-coverage libraries for single-cell DNA methylation analysis.
• The method facilitates cell type identification, genome-wide hemi-methylation profiling, and allele-resolved X-inactivation analysis.
• Combined data enabled identification of replicating cells and profiling of DNA methylation maintenance dynamics.

Conclusions:

• scDEEP-mC significantly advances single-cell epigenomic profiling capabilities.
• The method allows for deeper insights into DNA methylation regulation and cell-to-cell variability.
• High-complexity, efficient scWGBS library construction is key for exploring DNA methylation dynamics.