GSE126064
Global co-transcriptional splicing in Arabidopsis and the correlation with splicing regulation in mature RNAs
RNA splicing and spliceosome assembly in eukaryotes occur mainly during transcription. However, co-transcriptional splicing has not yet been explored in plants. Here, we showed that in Arabidopsis thaliana, nearly all introns undergo co-transcriptional splicing and this occurs with higher efficiency for introns in protein-coding genes than for noncoding RNAs. Co-transcriptional splicing efficiency correlates with density of 19 epigenetic modifications. Total intron number and intron position are two predominant sequence 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 trans-acting protein mutations 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. Our results not only uncovered widespread co-transcriptional splicing in Arabidopsis, but also uncovered features that may affect or be affected by co-transcriptional splicing efficiency. Overall design: To study the co-transcriptional splicing in Arabidopsis and possible roles at splicing factors, RNA-seq libraryies were contrusted using total tissue and chromatin fraction in wild type and mutants defective in splicing including mac3a mac3b and prl1 prl2.