Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology.
College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China.
Bioinformatics. 2019 Sep 1;35(17):3119-3126. doi: 10.1093/bioinformatics/btz038.
MicroRNA (miRNA) and alternative splicing (AS)-mediated post-transcriptional regulation has been extensively studied in most eukaryotes. However, the interplay between AS and miRNAs has not been explored in plants. To our knowledge, the overall profile of miRNA target sites in circular RNAs (circRNA) generated by alternative back splicing has never been reported previously. To address the challenge, we identified miRNA target sites located in alternatively spliced regions of the linear and circular splice isoforms using the up-to-date single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) and Illumina sequencing data in eleven plant species.
In total, we identified 399 401 and 114 574 AS events from linear and circular RNAs, respectively. Among them, there were 64 781 and 41 146 miRNA target sites located in linear and circular AS region, respectively. In addition, we found 38 913 circRNAs to be overlapping with 45 648 AS events of its own parent isoforms, suggesting circRNA regulation of AS of linear RNAs by forming R-loop with the genomic locus. Here, we present a comprehensive database of miRNA targets in alternatively spliced linear and circRNAs (ASmiR) and a web server for deposition and identification of miRNA target sites located in the alternatively spliced region of linear and circular RNAs. This database is accompanied by an easy-to-use web query interface for meaningful downstream analysis. Plant research community can submit user-defined datasets to the web service to search AS regions harboring small RNA target sites. In conclusion, this study provides an unprecedented resource to understand regulatory relationships between miRNAs and AS in both gymnosperms and angiosperms.
The readily accessible database and web-based tools are available at http://forestry.fafu.edu.cn/bioinfor/db/ASmiR.
Supplementary data are available at Bioinformatics online.
微小 RNA（miRNA）和选择性剪接（AS）介导的转录后调控已在大多数真核生物中得到广泛研究。然而，在植物中，AS 和 miRNAs 之间的相互作用尚未被探索。据我们所知，以前从未报道过通过选择性反向剪接产生的环状 RNA（circRNA）中 miRNA 靶位点的总体概况。为了解决这一挑战，我们使用最新的单分子实时（SMRT）异构体测序（Iso-Seq）和 Illumina 测序数据，在 11 种植物物种中鉴定了位于线性和环状剪接异构体的选择性剪接区域的 miRNA 靶位点。
我们总共从线性和环状 RNA 中鉴定出 399401 和 114574 个 AS 事件。其中，线性和环状 AS 区域分别有 64781 和 41146 个 miRNA 靶位点。此外，我们发现 38913 个 circRNAs 与自身亲本异构体的 45648 个 AS 事件重叠，这表明 circRNA 通过与基因组位置形成 R 环来调节线性 RNA 的 AS。在这里，我们提供了一个包含 miRNA 靶标在选择性剪接线性和环状 RNA 中的综合数据库（ASmiR）和一个用于存储和鉴定线性和环状 RNA 中选择性剪接区域的 miRNA 靶标的 Web 服务器。该数据库还附有一个易于使用的 Web 查询界面，用于进行有意义的下游分析。植物研究界可以向 Web 服务提交用户定义的数据集，以搜索含有小 RNA 靶标 AS 区域。总之，本研究提供了一个前所未有的资源，以了解 gymnosperms 和 angiosperms 中 miRNA 和 AS 之间的调控关系。
可在 http://forestry.fafu.edu.cn/bioinfor/db/ASmiR 访问易于使用的数据库和基于网络的工具。
补充数据可在生物信息学在线获得。
