scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation

Area of Science:

• Epigenetics
• Genomics
• Molecular Biology

Background:

• DNA methylation is a crucial epigenetic modification regulating gene expression, development, and genome stability.
• Single-cell whole-genome bisulfite sequencing (scWGBS) enables base-resolution interrogation of 5-methylcytosine (5mC) in individual cells.
• Existing scWGBS methods face challenges in cost-efficiency and scalability.

Purpose of the Study:

• To introduce a novel, scalable, and cost-effective library preparation method for scWGBS.
• To improve the throughput of single-cell DNA methylation analysis.
• To validate the accuracy and robustness of the new method.

Main Methods:

• Development of single-cell Splinted Ligation Adapter Tagging (scSPLAT) for scWGBS library preparation.
• Implementation of a pooling strategy to enhance sample preparation scale and throughput.
• Generation of scWGBS data from 225 single K562 cells and 309 single liver nuclei.

Main Results:

• scSPLAT demonstrates accuracy and robustness in DNA methylation profiling at single-cell resolution.
• The method facilitates higher scale and throughput compared to previous scWGBS strategies.
• Comparative analysis validates scSPLAT's performance against existing scWGBS techniques.

Conclusions:

• scSPLAT represents a significant advancement in scWGBS library preparation, addressing limitations in cost and yield.
• The method enables large-scale, high-throughput DNA methylation analysis in single cells.
• scSPLAT is a valuable tool for studying epigenetic heterogeneity and dynamics in biological systems.