The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammation Biology, Tianjin Key Laboratory of Medical Epigenetics, Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.
Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.
Nucleic Acids Res. 2022 Jan 7;50(D1):D356-D364. doi: 10.1093/nar/gkab917.
Alternative polyadenylation (APA) has been widely recognized as a crucial step during the post-transcriptional regulation of eukaryotic genes. Recent studies have demonstrated that APA exerts key regulatory roles in many biological processes and often occurs in a tissue- and cell-type-specific manner. However, to our knowledge, there is no database incorporating information about APA at the cell-type level. Single-cell RNA-seq is a rapidly evolving and powerful tool that enable APA analysis at the cell-type level. Here, we present a comprehensive resource, scAPAatlas (http://www.bioailab.com:3838/scAPAatlas), for exploring APA across different cell types, and interpreting potential biological functions. Based on the curated scRNA-seq data from 24 human and 25 mouse normal tissues, we systematically identified cell-type-specific APA events for different cell types and examined the correlations between APA and gene expression level. We also estimated the crosstalk between cell-type-specific APA events and microRNAs or RNA-binding proteins. A user-friendly web interface has been constructed to support browsing, searching and visualizing multi-layer information of cell-type-specific APA events. Overall, scAPAatlas, incorporating a rich resource for exploration of APA at the cell-type level, will greatly help researchers chart cell type with APA and elucidate the biological functions of APA.
可变聚腺苷酸化（APA）已被广泛认为是真核基因转录后调控的关键步骤。最近的研究表明，APA 在许多生物过程中发挥着关键的调节作用，并且通常以组织和细胞类型特异性的方式发生。然而，据我们所知，目前还没有一个包含细胞类型水平 APA 信息的数据库。单细胞 RNA-seq 是一种快速发展和强大的工具，可实现细胞类型水平的 APA 分析。在这里，我们提出了一个全面的资源 scAPAatlas（http://www.bioailab.com:3838/scAPAatlas），用于探索不同细胞类型中的 APA，并解释潜在的生物学功能。基于从 24 个人类和 25 个小鼠正常组织中精心整理的 scRNA-seq 数据，我们系统地鉴定了不同细胞类型的细胞类型特异性 APA 事件，并检查了 APA 与基因表达水平之间的相关性。我们还估计了细胞类型特异性 APA 事件与 microRNAs 或 RNA 结合蛋白之间的串扰。构建了一个用户友好的 Web 界面，用于支持浏览、搜索和可视化细胞类型特异性 APA 事件的多层信息。总的来说，scAPAatlas 整合了丰富的资源，用于探索细胞类型水平的 APA，将极大地帮助研究人员绘制 APA 与细胞类型的关系，并阐明 APA 的生物学功能。
