A comprehensive analysis of 3UTRs in Caenorhabditis elegans

Abstract

3Untranslated regions (3UTRs) are essential portions of genes containing elements necessary for pre-mRNA 3end processing and are involved in post-transcriptional gene regulation. Despite their importance, they remain poorly characterized in eukaryotes. Here, we have used a multi-pronged approach to extract and curate 3UTR data from 11533 publicly available datasets, corresponding to the entire collection of Caenorhabditis elegans transcriptomes stored in the NCBI repository from 2009 to 2023. We have also performed high throughput cloning pipelines to identify and validate rare 3UTR isoforms and incorporated and manually curated 3UTR isoforms from previously published datasets. This updated C. elegans 3UTRome (v3) is the most comprehensive resource in any metazoan to date, covering 97.4% of the 20362 experimentally validated protein-coding genes with refined and updated 3UTR boundaries for 23489 3UTR isoforms. We also used this novel dataset to identify and characterize sequence elements involved in pre-mRNA 3end processing and update miRNA target predictions. This resource provides important insights into the 3UTR formation, function, and regulation in eukaryotes.