A Comprehensive Analysis of 3-UTRs in Caenorhabditis elegans

Summary/Abstract3Untranslated 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 11,533 publicly available datasets, corresponding to the entire collection of C. elegans transcriptomes stored in the NCBI repository from 2009 to 2023, and present its complete 3UTRome dataset sequenced at single-base resolution. This updated C. elegans 3UTRome is the most comprehensive resource in any metazoan, covering 97.4% of the 20,362 experimentally validated protein-coding genes with refined and updated 3UTR boundaries for 23,489 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.