scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3′ scRNA-seq data

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-08-07 DOI:10.1186/s13059-025-03710-7

Ruiyan Hou, Yuanhua Huang

引用次数: 0

Abstract

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.

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scTail：从reads 1保存的3 ' scRNA-seq数据中精确检测聚腺苷化位点及其替代用途分析

3 ' scRNA-seq （3 ' scRNA-seq）的第一链读取（通常读取1）可以包含用于分析聚腺苷化位点（PAS）的信息丰富的cDNA，但经常被忽略或修剪。在这里，我们描述了一种计算方法，scTail，利用第一链读取来识别PAS，并利用第二链读取来量化其表达，从而能够检测PAS的替代使用。与其他方法相比，scTail检测PAS的精度更高，灵敏度也更高。此外，我们证明结合scTail和BRIE2可以发现不同生物过程中PAS的差异替代使用，包括癌症和时间序列发展，为PAS调控提供关键见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

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