Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans

Area of Science:

• Genomics and Molecular Biology
• Bioinformatics and Computational Biology

Background:

• Gene structure annotation in C. elegans remains incomplete, with ongoing discovery of gene variants via transcriptome studies.
• The extent of tolerated spurious splicing versus functional alternative splicing is a significant debate in the field.

Purpose of the Study:

• To increase the detection range of RNA isoforms and accurately measure splicing event abundance in C. elegans.
• To develop a method for distinguishing robust splicing events from biological noise using gene expression levels.
• To re-evaluate the prevalence of trans-splicing in the C. elegans genome.

Main Methods:

• Compiled a large dataset of 1682 C. elegans RNA-seq samples to enhance detection sensitivity.
• Developed an automated curation method integrating gene expression levels to filter spurious splicing events.
• Analyzed splice site conservation across nematode genomes and quantified trans-splicing events.

Main Results:

• Most splicing reads originate from reproducible events, but many junctions are supported by minimal read counts.
• Rarely used splice sites are more frequent in highly expressed genes and show lower conservation.
• Trans-splicing was confirmed for at least 84% of C. elegans protein-coding genes, particularly in higher expressed genes.

Conclusions:

• The study provides robustly annotated gene models with quantitative exon usage for the C. elegans genome.
• The findings suggest trans-splicing is widespread, though low-expression genes may be underrepresented in current RNA-seq data.
• The developed methods aid in discerning biologically relevant splicing from noise, improving gene annotation accuracy.