RNA splicing and spliceosome assembly in eukaryotes occur mainly during transcription. However, co-transcriptional splicing has not yet been explored in plants. Here, we built transcriptomes of nascent chromatin RNAs in Arabidopsis thaliana and showed that nearly all introns undergo co-transcriptional splicing, which occurs with higher efficiency for introns in protein-coding genes than for those in noncoding RNAs. Total intron number and intron position are two predominant features that correlate with co-transcriptional splicing efficiency, and introns with alternative 5′ or 3′ splice sites are less efficiently spliced. Furthermore, we found that mutations in genes encoding trans-acting proteins lead to more introns with increased splicing defects in nascent RNAs than in mature RNAs, and that introns with increased splicing defects in mature RNAs are inefficiently spliced at the co-transcriptional level. Collectively, our results not only uncovered widespread co-transcriptional splicing in Arabidopsis but also identified features that may affect or be affected by co-transcriptional splicing efficiency.

真核生物中的RNA剪接和剪接体组装主要在转录过程中发生。然而，尚未在植物中探索共转录剪接。在这里，我们在拟南芥中建立了新生染色质RNA的转录组，并显示几乎所有内含子都进行了共转录剪接，蛋白质编码基因中的内含子发生效率要高于非编码RNA中的内含子。总内含子数量和内含子位置是与共转录剪接效率相关的两个主要特征，而具有备选5'或3'剪接位点的内含子的剪接效率较低。此外，我们发现编码反式的基因中的突变作用蛋白比成熟RNA导致更多的内含子，其中新生的RNA剪接缺陷增加，而成熟RNA中的剪接缺陷增加的内含子在共转录水平上被低效剪接。总的来说，我们的结果不仅发现了拟南芥中广泛的共转录剪接， 而且还鉴定了可能影响共转录剪接效率或受其影响的特征。