Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.
National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian 3611002, China.
Plant Physiol. 2020 Jan;182(1):228-242. doi: 10.1104/pp.19.00943. Epub 2019 Nov 25.
Alternative cleavage and polyadenylation (APA) is increasingly recognized as an important regulatory mechanism in eukaryotic gene expression and is dynamically modulated in a developmental, tissue-specific, or environmentally responsive manner. Given the functional importance of APA and the rapid accumulation of APA sites in plants, a comprehensive and easily accessible APA site database is necessary for improved understanding of APA-mediated gene expression regulation. We present a database called PlantAPAdb that catalogs the most comprehensive APA site data derived from sequences from diverse 3' sequencing protocols and biological samples in plants. Currently, PlantAPAdb contains APA sites in six species, ( and ), Arabidopsis (), , , , and APA sites in PlantAPAdb are available for bulk download and can be queried in a Google-like manner. PlantAPAdb provides rich information of the whole-genome APA sites, including genomic locations, heterogeneous cleavage sites, expression levels, and sample information. It also provides comprehensive poly(A) signals for APA sites in different genomic regions according to distinct profiles of cis-elements in plants. In addition, PlantAPAdb contains events of 3' untranslated region shortening/lengthening resulting from APA, which helps to understand the mechanisms underlying systematic changes in 3' untranslated region lengths. Additional information about conservation of APA sites in plants is also available, providing insights into the evolutionary polyadenylation configuration across species. As a user-friendly database, PlantAPAdb is a large and extendable resource for elucidating APA mechanisms, APA conservation, and gene expression regulation.
可变剪接和多聚腺苷酸化（APA）越来越被认为是真核基因表达的重要调控机制，并且以发育、组织特异性或环境响应的方式动态调节。鉴于 APA 的功能重要性以及植物中 APA 位点的快速积累，需要一个全面且易于访问的 APA 位点数据库，以提高对 APA 介导的基因表达调控的理解。我们介绍了一个名为 PlantAPAdb 的数据库，它对来自不同 3' 测序方案和植物生物样本的序列中提取的最全面的 APA 位点数据进行了编目。目前，PlantAPAdb 包含六个物种的 APA 位点，包括 (和)、Arabidopsis (拟南芥)、,,, 和 。在 PlantAPAdb 中，APA 位点可批量下载，并可采用类似于谷歌的方式进行查询。PlantAPAdb 提供了全基因组 APA 位点的丰富信息，包括基因组位置、异质切割位点、表达水平和样本信息。它还根据植物中顺式元件的不同特征，为不同基因组区域的 APA 位点提供了全面的 poly(A) 信号。此外，PlantAPAdb 还包含了由于 APA 导致的 3' 非翻译区缩短/延长的事件，这有助于理解 3' 非翻译区长度系统变化的机制。还提供了植物中 APA 位点保守性的附加信息，为跨物种的进化多腺苷酸化配置提供了深入了解。作为一个用户友好的数据库，PlantAPAdb 是一个阐明 APA 机制、APA 保守性和基因表达调控的大型可扩展资源。
