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PolyA_DB v4:在人类和小鼠基因组中使用3'末端和长读测序数据进行系统的PolyA位点识别和异型注释

Shan Yu¹, Wei Chun Chen¹, Luyang Wang¹

¹Genome Regulation and Cell Signalling Program, Ellen and Ronald Caplan Cancer Center, The Wistar Institute, Philadelphia, PA 19104, United States.

Nucleic acids research

|November 29, 2025

概括

PolyA_DB 4 版本显著扩展了哺乳动物基因组中裂变和多化位点 (PAS) 的数据库. 这次更新通过识别数百万个新的PAS并通过长期读取的RNA测序数据验证它们,提高了我们对替代多基化 (APA) 的理解.

科学领域:

基因组学就是基因组学.
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

细胞RNA的3'端是由裂变和多化位 (PAS) 所定义的.
替代多基化 (APA) 导致单基因的多种RNA异型.
准确的PAS注释对于理解RNA生物学至关重要.

研究的目的:

为了呈现PolyA_DB版本4,一个更新的哺乳动物裂变和多化部位 (PAS) 数据库.
提高人类和小鼠基因组中PAS注释的覆盖范围和准确性.
整合和分析长时间读取的RNA测序数据,用于PAS验证和APA事件亚型化.

主要方法:

使用3'区域提取和深度测序加 (3'READS+) 方法对人类和小鼠的转录组数据进行详尽的挖掘.
在人类和小鼠基因组中识别和注释大约140万个PAS.
鉴定PAS与长读RNA测序 (LR-RNA-seq) 转录末端站点 (TES) 的比较和整合.

主要成果:

PolyA_DB v4 在人类和小鼠基因组中识别了约140万个PAS,覆盖率显著增加.
整个PAS集合 (Max集合) 的20%与LR-RNA-seq TES一致.
LR-RNA-seq数据补充了基于RefSeq的PAS分配,并有助于亚型化APA事件.

结论:

PolyA_DB v4为哺乳动物PAS提供了一个全面的资源,大大提高了覆盖范围和准确性.
对于验证PAS和表征APA事件,LR-RNA-seq数据非常有价值,尽管潜在的文物需要仔细考虑.
更新的数据库有助于研究RNA处理,基因调节以及APA异型的功能影响.

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