Hou Ruiyan, Huang Yuanhua
School of Biomedical Sciences, University of Hong Kong, Hong Kong SAR, China.
Department of Statistics and Actuarial Science, University of Hong Kong, Hong Kong SAR, China.
Genome Biol. 2025 Aug 7;26(1):236. doi: 10.1186/s13059-025-03710-7.
The first-strand reads (often reads 1) of three-prime single-cell RNA-seq (3' scRNA-seq) can contain informative cDNA for analysis of polyadenylation sites (PAS), but are often overlooked or trimmed. Here, we describe a computational method, scTail, to identify PAS using first-strand reads and quantify its expression leveraging second-strand reads, consequently enabling detection of alternative PAS usage. Compared with other methods, scTail detects PAS more precisely and retains high sensitivity. Furthermore, we demonstrated that combining scTail and BRIE2 can discover differential alternative PAS usage in various biological processes including cancers and time-series development, giving critical insight into PAS regulation.
三端单细胞RNA测序（3' scRNA-seq）的第一链 reads（通常为reads 1）可能包含用于分析聚腺苷酸化位点（PAS）的信息性cDNA，但常常被忽视或修剪。在这里，我们描述了一种计算方法scTail，用于使用第一链reads识别PAS，并利用第二链reads对其表达进行定量，从而能够检测替代性PAS使用情况。与其他方法相比，scTail能更精确地检测PAS并保持高灵敏度。此外，我们证明将scTail和BRIE2相结合，可以在包括癌症和时间序列发育在内的各种生物学过程中发现差异性替代性PAS使用情况，从而深入了解PAS调控。
