Landscape and regulation of alternative splicing and alternative polyadenylation in a plant pathogenic fungus
Landscape and regulation of alternative splicing and alternative polyadenylation in a plant pathogenic fungus
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植物病原真菌中选择性剪接和选择性多腺苷酸化的景观和调控
DOI：
10.1111/nph.18164
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发表时间：
2022-05-11
期刊：
影响因子：
9.4
通讯作者：
Liu, Huiquan
中科院分区：
文献类型：
--
作者：
Lu, Ping;Chen, Daipeng;Liu, Huiquan
选择性剪接（AS）和选择性多腺苷酸化（APA）对高等真核生物中基因表达的调节有显着贡献。然而，它们对丝状真菌的生物学影响很大程度上未知。在这里，我们结合了 PacBio 同工型测序和多种组织的链特异性 RNA 测序以及突变体表征，揭示了禾谷镰刀菌中 AS 和 APA 的景观和调控。我们生成了包含来自 17 189 个基因的 51 617 个亚型的转录本注释。总共，分别有 4997 个和 11 133 个基因被选择性剪接和聚腺苷酸化。大多数 AS 事件都会改变编码序列。出乎意料的是，含有提前终止密码子的 AS 转录本对无义介导的信使 RNA 衰变不敏感。与酵母和动物不同，远端 APA 位点具有强信号，但近端 APA 亚型在禾谷镰刀菌中高度表达。 3'端加工因子FgRNA15、FgHRP1和FgFIP1在促进近端APA位点使用和内含子剪接中发挥作用。在老年和静止组织中观察到内含子包含和远端 APA 位点使用的全基因组增加以及剪接体和 3'-末端加工因子的下调，表明内含子包含和 3'-非翻译区延长是调节真菌衰老和休眠的新机制。这项研究为丝状真菌中 AS 和 APA 的复杂性和调控提供了新的见解。
Alternative splicing (AS) and alternative polyadenylation (APA) contribute significantly to the regulation of gene expression in higher eukaryotes. Their biological impact in filamentous fungi, however, is largely unknown. Here we combine PacBio Isoform-Sequencing and strand-specific RNA-sequencing of multiple tissues and mutant characterization to reveal the landscape and regulation of AS and APA in Fusarium graminearum. We generated a transcript annotation comprising 51 617 isoforms from 17 189 genes. In total, 4997 and 11 133 genes are alternatively spliced and polyadenylated, respectively. Majority of the AS events alter coding sequences. Unexpectedly, the AS transcripts containing premature-termination codons are not sensitive to nonsense-mediated messenger RNA decay. Unlike in yeasts and animals, distal APA sites have strong signals, but proximal APA isoforms are highly expressed in F. graminearum. The 3 '-end processing factors FgRNA15, FgHRP1, and FgFIP1 play roles in promoting proximal APA site usage and intron splicing. A genome-wide increase in intron inclusion and distal APA site usage and downregulation of the spliceosomal and 3 '-end processing factors were observed in older and quiescent tissues, indicating intron inclusion and 3 '-untranslated region lengthening as novel mechanisms in regulating aging and dormancy in fungi. This study provides new insights into the complexity and regulation of AS and APA in filamentous fungi.