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The Features and Regulation of Co-transcriptional Splicing in Arabidopsis.
Molecular Plant ( IF 27.5 ) Pub Date : 2019-11-21 , DOI: 10.1016/j.molp.2019.11.004
Danling Zhu 1 , Fei Mao 2 , Yuanchun Tian 2 , Xiaoya Lin 3 , Lianfeng Gu 4 , Hongya Gu 3 , Li-Jia Qu 3 , Yufeng Wu 2 , Zhe Wu 1
Affiliation  

Precursor mRNA (pre-mRNA) splicing is essential for gene expression in most eukaryotic organisms. Previous studies from mammals, Drosophila, and yeast show that the majority of splicing events occurs co-transcriptionally. In plants, however, the features of co-transcriptional splicing (CTS) and its regulation still remain largely unknown. Here, we used chromatin-bound RNA sequencing to study CTS in Arabidopsis thaliana. We found that CTS is widespread in Arabidopsis seedlings, with a large proportion of alternative splicing events determined co-transcriptionally. CTS efficiency correlated with gene expression level, the chromatin landscape and, most surprisingly, the number of introns and exons of individual genes, but is independent of gene length. In combination with enhanced crosslinking and immunoprecipitation sequencing analysis, we further showed that the hnRNP-like proteins RZ-1B and RZ-1C promote efficient CTS globally through direct binding, frequently to exonic sequences. Notably, this general effect of RZ-1B/1C on splicing promotion is mainly observed at the chromatin level, not at the mRNA level. RZ-1C promotes CTS of multiple-exon genes in association with its binding to regions both proximal and distal to the regulated introns. We propose that RZ-1C promotes efficient CTS of genes with multiple exons through cooperative interactions with many exons, introns, and splicing factors. Our work thus reveals important features of CTS in plants and provides methodologies for the investigation of CTS and RNA-binding proteins in plants.



中文翻译:

拟南芥共转录剪接的特征和调控。

前体mRNA(pre-mRNA)剪接对于大多数真核生物中的基因表达至关重要。先前来自哺乳动物,果蝇和酵母的研究表明,大多数剪接事件是共转录发生的。然而,在植物中,共转录剪接(CTS)的功能及其调控仍然很大程度上未知。在这里,我们使用了染色质结合的RNA测序来研究拟南芥中的CTS 。我们发现CTS在拟南芥中很普遍幼苗,其中很大比例的选择性剪接事件是通过共转录确定的。CTS效率与基因表达水平,染色质分布以及单个基因的内含子和外显子数量相关,但与基因长度无关。结合增强的交联和免疫沉淀测序分析,我们进一步表明,hnRNP样蛋白RZ-1B和RZ-1C通过直接结合(通常与外显子序列结合)在全球范围内促进高效CTS。值得注意的是,RZ-1B / 1C对剪接促进的一般作用主要在染色质水平上观察到,而不是在mRNA水平上观察到。RZ-1C与其受调节内含子近端和远端区域的结合有关,可促进多外显子基因的CTS。我们建议RZ-1C通过与许多外显子,内含子和剪接因子的协同相互作用来促进具有多个外显子的基因的高效CTS。因此,我们的工作揭示了植物中CTS的重要特征,并为研究植物中CTS和RNA结合蛋白提供了方法。

更新日期:2019-11-21
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