The Features and Regulation of Co-transcriptional Splicing in Arabidopsis

Abstract

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.

Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana

“…We propose that these changes in nucleosome occupancy may provide the basic definition to exons and introns to coordinate RNAPII processivity. However, it is apparent that the splicing process is also fine‐tuned by various trans ‐regulatory factors and histone modifications under variable growth and stress conditions (Kindgren et al ., 2019; Zhu et al ., 2020). Our data support this notion, and it is likely that higher nucleosome occupancy may regulate RNAPII accumulation around splice sites and enable SF recruitment to facilitate and/or modulate splicing variation.…”

“…Recent evidence shows that alternative splicing (AS) regulation is a key gene regulatory mechanism in plants (Calixto et al ., 2018; Filichkin et al ., 2018; Jabre et al ., 2019). In plants and animals, AS is regulated co‐transcriptionally (Brody et al ., 2011; Tilgner et al ., 2012; Li et al ., 2020; Zhu et al ., 2020). RNA polymerase II (RNAPII) speed during transcription may be affected by the chromatin state that in turn determines AS outcomes (Alexander et al ., 2010; Ullah et al ., 2018; Zhu et al ., 2018).…”

“…Remarkably, sequencing of the chromatin‐bound nascent RNAs in Arabidopsis revealed that almost all introns are spliced co‐transcriptionally and the efficiency of intron removal is more robust in protein‐coding genes than noncoding RNAs (Li et al ., 2020). Furthermore, it was also demonstrated that co‐transcriptional splicing (CTS) efficiency is dependent on the number of exons but not gene length (Zhu et al ., 2020). Therefore, appropriate exon–intron definition may be important for CTS in Arabidopsis (Li et al ., 2020).…”

Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana

“…Furthermore, CTS was found to be the predominant mode of splicing in different species, including humans, Drosophila and budding yeast (Ameur et al, 2011;Khodor et al, 2011;Oesterreich et al, 2016). Recently, it was found that this also occurs in A. thaliana (Li et al, 2020;Zhu et al, 2020). These findings suggest that for circadian genes, constitutive splicing would also occur in a circadian fashion, as it would occur co-transcriptionally.…”

“…This occurs more efficiently for introns of protein-coding genes, and less efficiently for introns with AS sites (Li et al, 2020). Additionally, it has been found that CTS is independent of gene length, but rather correlates with gene expression level, chromatin landscape, and total number of introns and exons of the gene in question (Zhu et al, 2020). Through this process, different functional mRNAs can arise from the transcription of the same gene, ultimately expanding the repertoire of protein products that can be encoded by a single gene (Kornblihtt et al, 2013;Saldi et al, 2016).…”