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Genome Res. 2019 Dec;29(12):2104-2116. doi: 10.1101/gr.254839.119. Epub 2019 Nov 19.

The C. elegans 3' UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3'-UTR biology, and miRNA targeting.

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Molecular and Cellular Biology Graduate Program, School of Life Sciences, Tempe, Arizona 85287.
Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona 85281, USA.
Barrett, The Honors College, Arizona State University, Tempe, Arizona 85281, USA.
Center for Applied Structural Discovery, The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA.


3' Untranslated regions (3' UTRs) of mRNAs emerged as central regulators of cellular function because they contain important but poorly characterized cis-regulatory elements targeted by a multitude of regulatory factors. The model nematode Caenorhabditis elegans is ideal to study these interactions because it possesses a well-defined 3' UTRome. To improve its annotation, we have used a genome-wide bioinformatics approach to download raw transcriptome data for 1088 transcriptome data sets 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 ultradeep 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 ultraresolution 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 data set 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 data set 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.

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