Systematic evaluation of tools used for single-cell m6A identification

作者：Yueqi Li, Xinyue Xu, Mingcong Chen, Meng Jun, Dan Jiang, Yi Bao, Yelongzi Cao, Yajing Chen, Chun Chang, Shiou Yih Lee, Yafei Chen, Jia Lü, Chen Yang, Xiaoping Lv, Hao Liang, Kaikai Meng, Sanqi An · 发表于：Communications Biology · 年份：2025 · DOI：10.1038/s42003-025-09246-7 · 被引用次数：1 · 研究领域：RNA modifications and cancer、Cancer-related gene regulation、Epigenetics and DNA Methylation

N6-methyladenosine (m6A) modifications are prevalent across all mammals and represent the most abundant type of epigenetic modification. With advancements in research, new methods for single-cell m6A modification sequencing and prediction have continuously emerged. These methods provide researchers with powerful tools to explore the landscape of epigenetic modifications at the single-cell level. However, challenges such as operational complexity, limited sensitivity, resolution, and consistency across different techniques remain major obstacles for researchers in this field. In this study, we compared four representative single-cell m6A sequencing and prediction methods based on different principles. We also developed a single-cell m6A database, which is freely accessible online. The database allows users to search for the localization and modification levels of single-cell m6A modifications in human and mouse species on the basis of these methods. It also offers cell definitions, data visualization, and data download options. Additionally, we applied Scm6A to single-cell transcriptome data across cancers and spatial transcriptome data from UCEC to predict and visualize m6A modifications, demonstrating its unique superior performance. Comparison of single-cell m6A methods and development of a freely accessible database, Scm6A, enabling prediction and visualization of m6A modifications across human and mouse single-cell and spatial transcriptomes.