ASAPA: a bioinformatic pipeline based on Iso-Seq that identifies the links among alternative splicing, alternative transcription initiation and alternative polyadenylation
文献类型： 外文期刊
作者： Wang, Fei 1 ; Jin, Zhongxin 2 ; Wang, Shengnan 1 ; Yang, Longcheng 1 ; Fan, Zongbao 1 ; Yao, Yuxin 1 ;
作者机构： 1.Shandong Agr Univ, Coll Hort Sci & Engn, Collaborat Innovat Ctr Fruit & Vegetable Qual & Ef, State Key Lab Crop Biol, Tai An 271018, Shandong, Peoples R China
2.Chinese Acad Trop Agr Sci, Sanya Res Inst, Natl Key Lab Trop Crop Breeding, Haikou, Peoples R China
关键词： Alternative splicing; Alternative transcription initiation; Alternative polyadenylation; Correlation analysis
期刊名称：FUNCTIONAL & INTEGRATIVE GENOMICS （ 影响因子：2.9； 五年影响因子：3.3 ）
ISSN： 1438-793X
年卷期： 2024 年 24 卷 2 期
页码：
收录情况： SCI
摘要： Background: Although the events associated with alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI) can be identified by many approaches based on isoform sequencing (Iso-Seq), these analyses are generally independent of each other and the links between these events are still rarely mentioned. However, an interdependency analysis can be achieved because the transcriptional start site, splice sites and polyA site could be simultaneously included in a long, full-length read from Iso-Seq. Results: We create ASAPA pipeline that enables streamlined analysis for a robust detection of potential links among AS, ATI and APA using Iso-Seq data. We tested this pipeline using Arabidopsis data and found some interesting results: some adjacent introns tend to be simultaneously spliced or retained; coupling between AS and ATI or APA is limited to the initial or terminal intron; and ATI and APA are potentially linked in some special cases. Conclusion: Our pipeline enables streamlined analysis for a robust detection of potential links among AS, ATI and APA using Iso-Seq data, which is conducive to a better understanding of transcription landscape generation.
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