The Features and Regulation of Co-transcriptional Splicing in Arabidopsis
The Features and Regulation of Co-transcriptional Splicing in Arabidopsis
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拟南芥共转录剪接的特征及调控
DOI：
10.1016/j.molp.2019.11.004
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发表时间：
2020-02-03
期刊：
影响因子：
27.5
通讯作者：
Wu, Zhe
中科院分区：
文献类型：
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作者：
Zhu, Danling;Mao, Fei;Wu, Zhe
前体mRNA（pre-mRNA）剪接对于大多数真核生物中的基因表达是必需的。先前对哺乳动物、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）的特点和它的调控仍然在很大程度上未知。在这里，我们使用染色质结合RNA测序研究拟南芥CTS。我们发现，CTS是广泛存在于拟南芥幼苗，有很大比例的选择性剪接事件确定共转录。CTS效率与基因表达水平，染色质景观，最令人惊讶的是，单个基因的内含子和外显子的数量相关，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，经常是外显子序列，促进有效的CTS全球。值得注意的是，RZ-1B/1C对剪接促进的这种一般作用主要在染色质水平上观察到，而不是在mRNA水平上。RZ-1C促进多外显子基因的CTS，与其结合到受调控内含子的近端和远端区域有关。我们提出RZ-1C通过与许多外显子、内含子和剪接因子的合作相互作用促进具有多个外显子的基因的有效CTS。因此，我们的工作揭示了重要功能的CTS在植物中，CTS和RNA结合蛋白的研究提供了方法。
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.