Systematic evaluation of tools used for single-cell m⁶A identification

Area of Science:

• Epigenetics and Molecular Biology
• Genomics and Bioinformatics

Background:

• N6-methyladenosine (m⁶A) is the most abundant epigenetic modification in mammals.
• Advancing single-cell sequencing methods offers insights into epigenetic landscapes.
• Challenges in current single-cell m⁶A techniques include complexity, sensitivity, and consistency.

Purpose of the Study:

• To compare four representative single-cell m⁶A sequencing and prediction methods.
• To develop a freely accessible online database for single-cell m⁶A modifications.
• To evaluate the performance of a new tool, Scm⁶A, in analyzing cancer and UCEC data.

Main Methods:

• Comparative analysis of four distinct single-cell m⁶A sequencing and prediction methodologies.
• Development of a comprehensive online database for single-cell m⁶A data.
• Application of Scm⁶A to single-cell transcriptome and spatial transcriptome data.

Main Results:

• Identification of strengths and limitations across different single-cell m⁶A techniques.
• Establishment of a user-friendly database for searching m⁶A localization and modification levels in humans and mice.
• Demonstration of Scm⁶A's superior performance in predicting and visualizing m⁶A modifications in cancer and UCEC datasets.

Conclusions:

• The developed database facilitates research on single-cell m⁶A modifications.
• Scm⁶A provides a powerful tool for analyzing m⁶A patterns in complex biological contexts.
• This work addresses key challenges in the field, enhancing the study of epigenetic regulation at the single-cell level.