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PASSpedia:在单细胞分辨率下跨越不同物种的多基化站点数据库

Pei-Hong Zhang^1,2, Hua Feng¹, Xu-Kai Ma¹

¹Center for Molecular Medicine, Children's Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.

Genomics, proteomics & bioinformatics

|September 23, 2025

概括

这项研究使用scRNA-seq数据的SCAPTURE v2工具对七种物种的多基化位点 (PAS) 使用情况进行了分析. 它揭示了特定物种的PAS偏好,并介绍了PASSpedia,这是PAS分析的全面数据库.

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:

聚基化位点 (PAS) 选择对于基因表达调节至关重要.
在RNA-seq数据中使用3'标签测序来研究替代多基化 (APA) 异形表达.
在单细胞RNA测序 (scRNA-seq) 中进行PAS分析的先前方法存在局限性.

研究的目的:

升级SCAPTURE管道 (v2) 以进行全面的PAS分析.
通过使用大型scRNA-seq数据集,分析七种物种的PAS使用情况.
创建一个公开可访问的数据库 (PASSpedia),用于跨物种PAS比较.

主要方法:

将基于深度学习的 SCAPTURE v2 管道应用于基于 1330 3' 标签的 scRNA-seq 数据集.
通过使用长读序列数据验证了SCAPTURE的单细胞PAS分析准确性.
对比不同物种的PAS使用模式,包括人类和老鼠.

主要成果:

在单细胞分辨率下生成了七种物种的全面PAS景观.
证明了SCAPTURE v2的高精度,识别了新的PASS.
确定了不同的,特定于物种的PAS使用偏好,独立于基因表达保护.

结论:

SCAPTURE v2准确地描述了不同物种的单细胞PAS使用情况.
PASSpedia为PAS比较分析提供了一个宝贵的资源.
特定物种的APA有助于生物多样性超越保存的基因表达.

关键词:

替代性的排泄方式是排泄.数据库数据库数据库是一个数据库.保护多个物种的保护.聚亚脱化聚亚脱化一个单细胞RNA-seqq.

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