SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China.
State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China.
Mol Plant. 2020 Feb 3;13(2):278-294. doi: 10.1016/j.molp.2019.11.004. Epub 2019 Nov 21.
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.
前体信使 RNA（pre-mRNA）剪接对于大多数真核生物的基因表达至关重要。来自哺乳动物、果蝇和酵母的先前研究表明，大多数剪接事件发生在转录过程中。然而，在植物中，共转录剪接（CTS）及其调控的特征在很大程度上仍然未知。在这里，我们使用染色质结合 RNA 测序来研究拟南芥中的 CTS。我们发现 CTS 在拟南芥幼苗中广泛存在，其中很大一部分可变剪接事件是共转录决定的。CTS 效率与基因表达水平、染色质景观以及最令人惊讶的是，个别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，通常结合到外显子序列，全局促进 CTS。值得注意的是，RZ-1B/1C 对剪接促进的这种普遍影响主要发生在染色质水平，而不是在 mRNA 水平。RZ-1C 通过与其结合到受调节内含子的近端和远端区域，促进多外显子基因的 CTS。我们提出，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，促进具有多个外显子的基因的有效 CTS。我们的工作因此揭示了植物中 CTS 的重要特征，并为植物中 CTS 和 RNA 结合蛋白的研究提供了方法。
