Quantitative analysis of dynamic Spliced Leader Trans-Splicing in Caenorhabditis elegans

Spliced Leader Trans-Splicing (SLTS) is an important process in Caenohabditis elegans transcript maturation that is required for viability. However, the role it plays in development remains unclear. We explore the dynamic use of SLTS during C. elegans development. Using PacBio Iso-Seq data and WormBase annotations, we characterized SLTS Acceptor Sites (SLTS ASs) in full-length transcripts and predicted putative SLTS ASs for 98.8% of annotated protein-coding transcripts. By taking advantage of over 1000 publicly available RNA-seq datasets, we quantified the level of SL1 and SL2 SLTS and found evidence supporting SLTS for 70.3% of annotated protein-coding transcripts, which was consistent with previous research. We found cases of dynamics during embryogenesis, including those where the dominant SL changed, which suggests that SLTS is dynamic and may be regulated. This improves the current understanding of the role of SLTS in gene expression during development and provides insight into the dynamic nature of operons.