Trans-splicing occurs when two distinct RNA molecules, which originate from different genomic regions, are spliced together. This phenomenon occurs in a wide range of organisms, including nematodes and mammals. In C. elegans, a particular form of trans-splicing takes place. During the post-transcriptional processing of pre-mRNA, a highly conserved splice leader sequence is spliced to the 5’ end of transcripts. Earlier efforts that quantified trans-splicing in C. elegans suggest that 70% of genes are trans-spliced. The goal of this research is to examine whether trans-splicing in C. elegans is static or dynamic in developmental stages in different tissue types and to ascertain the functional impact of trans-splicing in C. elegans. In this project, we examined trans-splicing events for all genes and study the dynamics of trans-splicing in different conditions, using Iso-seq data we have generated and taking advantage of existing RNA-seq data generated by the modENCODE projects.
Our research used a combination of computational analysis and bioinformatics software to characterize trans-splicing events. We used Iso-seq data to study the nature of trans-splicing events in the context of full-length transcripts, the results of which were used to determine parameters for predicting and annotating trans-splicing acceptor sites. We predicted candidate trans-splicing acceptor sites based on the genome sequences and location of trans-splicing sites. Using RNA-seq data and the genome-sequence-based prediction of trans-splicing acceptor sites, we annotated trans-splicing events under various conditions, including developmental stages and tissue types. These results enabled us to compare the trans-splicing status across stages and conditions so that we can elucidate the dynamics of trans-splicing activities. Our analysis revealed that trans-splicing in C. elegans is a dynamic and regulated process, which may play a role in maintaining the level of translated genes. In this presentation, we will elaborate a genome-wide analysis of trans-splicing in C. elegans, with a focus on the dynamics of trans-splicing, tissue- and developmental-stage specific trans-splicing, and constitutive trans-splicing, aiming to elucidate the functional impact of trans-splicing in C. elegans.