Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals.
Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals.
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拟南芥中跨组织的替代剪接景观和压力条件突出了动物的主要功能差异。
DOI：
10.1186/s13059-020-02258-y
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发表时间：
2021-01-14
期刊：
影响因子：
12.3
通讯作者：
Irimia M
中科院分区：
文献类型：
--
作者：
Martín G;Márquez Y;Mantica F;Duque P;Irimia M
选择性剪接（AS）是多细胞生物中广泛存在的调节机制。植物中的大量转录组学和单基因研究已经研究了 AS 对特定条件（尤其是环境胁迫）的响应，揭示了调节基因表达的大量内含子保留。然而，目前仍缺乏对比应激反应和组织特异性 AS 模式并直接与动物模型进行比较的综合研究。我们为拟南芥生成了大量资源 PastDB，其中包括跨组织、发育和环境条件（包括非生物和生物胁迫）的 AS 和基因表达定量。对这些数据集的统一分析表明，拟南芥显示出高水平的 AS，与果蝇类似，并且与动物相比，拟南芥不成比例地使用 AS 来进行应激反应。我们确定了受应激或组织间的 AS 或转录特异性调节的核心基因组，这是这些基因的基因组特征紧密反映的调节专门化。出乎意料的是，非内含子保留事件，包括外显子跳跃，在拟南芥的受调控 AS 组中出现过多，也很大程度上参与通过 NMD 和 uORF 包含来调节基因表达。非内含子保留事件在植物中的功能可能被低估。 AS 构成了一个独特的调节层，在内部和外部刺激下控制基因表达，其靶基因和主调节因子在基因组水平上硬连线，以特异性地进行转录后调节。鉴于与动物相比，AS 在对不同应激的反应中具有更高的相关性，这种分子硬连线可能是拟南芥适当环境反应所必需的。在线版本包含可在 10.1186/s13059-020-02258-y 获取的补充材料。
Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing. We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion. Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana. The online version contains supplementary material available at 10.1186/s13059-020-02258-y.
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影响因子：
7
作者：
Braunschweig U;Barbosa-Morais NL;Pan Q;Nachman EN;Alipanahi B;Gonatopoulos-Pournatzis T;Frey B;Irimia M;Blencowe BJ
通讯作者：
Blencowe BJ
影响因子：
10.7
作者：
Derelle, Romain;Philippe, Herve;Colbourne, John K.
通讯作者：
Colbourne, John K.
影响因子：
7.2
作者：
Coolen, Silvia;Proietti, Silvia;Van Wees, Saskia C. M.
通讯作者：
Van Wees, Saskia C. M.
影响因子：
7.2
作者：
Cheng, Chia-Yi;Krishnakumar, Vivek;Town, Christopher D.
通讯作者：
Town, Christopher D.
影响因子：
3.9
作者：
Hu, Qiwen;Merchante, Catharina;Heber, Steffen
通讯作者：
Heber, Steffen