Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina.
Plant J. 2020 Jul;103(2):889-902. doi: 10.1111/tpj.14776. Epub 2020 May 18.
The circadian clock of Arabidopsis thaliana controls many physiological and molecular processes, allowing plants to anticipate daily changes in their environment. However, developing a detailed understanding of how oscillations in mRNA levels are connected to oscillations in co/post-transcriptional processes, such as splicing, has remained a challenge. Here we applied a combined approach using deep transcriptome sequencing and bioinformatics tools to identify novel circadian-regulated genes and splicing events. Using a stringent approach, we identified 300 intron retention, eight exon skipping, 79 alternative 3' splice site usage, 48 alternative 5' splice site usage, and 350 multiple (more than one event type) annotated events under circadian regulation. We also found seven and 721 novel alternative exonic and intronic events. Depletion of the circadian-regulated splicing factor AtSPF30 homologue resulted in the disruption of a subset of clock-controlled splicing events. Altogether, our global circadian RNA-seq coupled with an in silico, event-centred, splicing analysis tool offers a new approach for studying the interplay between the circadian clock and the splicing machinery at a global scale. The identification of many circadian-regulated splicing events broadens our current understanding of the level of control that the circadian clock has over this co/post-transcriptional regulatory layer.
拟南芥的生物钟控制着许多生理和分子过程，使植物能够预测环境的日常变化。然而，要详细了解 mRNA 水平的波动如何与剪接等转录后过程的波动相联系，一直是一个挑战。在这里，我们应用了一种结合深度转录组测序和生物信息学工具的综合方法来鉴定新的生物钟调节基因和剪接事件。使用严格的方法，我们鉴定出 300 个内含子保留、8 个外显子跳过、79 个 3'剪接位点使用、48 个 5'剪接位点使用和 350 个多重（一种以上事件类型）注释的生物钟调节事件。我们还发现了 7 个和 721 个新的外显子和内含子替代事件。生物钟调节剪接因子 AtSPF30 同源物的耗竭导致了一部分时钟控制剪接事件的破坏。总的来说，我们的全局生物钟 RNA-seq 与基于计算的、以事件为中心的剪接分析工具相结合，为在全局范围内研究生物钟和剪接机制之间的相互作用提供了一种新方法。许多生物钟调节剪接事件的鉴定拓宽了我们对生物钟对这个转录后调控层的控制程度的现有认识。
