The C. elegans 3’-UTRome V2: an updated genomic resource to study 3’-UTR biology

Abstract

3-Untranslated Regions (3-UTRs) of mRNAs emerged as central regulators of cellular function as they contain important but poorly-characterized cis-regulatory elements targeted by a multitude of regulatory factors. The model nematode C. elegans is ideal to study these interactions since it possesses a well-defined 3-UTRome. In order to improve its annotation, we have used a genomics approach to download raw transcriptome data for 1,088 transcriptome datasets corresponding to the entire collection of C. elegans trancriptomes from 2015 to 2018 from the Sequence Read Archive at the NCBI. We then extracted and mapped high-quality 3-UTR data at ultra-deep coverage. Here we describe and release to the community the updated version of the worm 3-UTRome, which we named 3-UTRome v2. This resource contains high-quality 3-UTR data mapped at single base ultra-resolution for 23,084 3-UTR isoform variants corresponding to 14,788 protein-coding genes and is updated to the latest release of WormBase. We used this dataset to study and probe principles of mRNA cleavage and polyadenylation in C. elegans. The worm 3-UTRome v2 represents the most comprehensive and high-resolution 3-UTR dataset available in C. elegans and provides a novel resource to investigate the mRNA cleavage and polyadenylation reaction, 3-UTR biology and miRNA targeting in a living organism.