Pervasive mRNA uridylation in fission yeast is catalysed by both Cid1 and Cid16 terminal uridyltransferases.

Autor: Lipińska-Zubrycka L; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland., Grochowski M; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland., Bähler J; Institute of Healthy Ageing and Research Department of Genetics, Evolution & Environment, University College London, London, United Kingdom., Małecki M; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2023 May 23; Vol. 18 (5), pp. e0285576. Date of Electronic Publication: 2023 May 23 (Print Publication: 2023).
DOI: 10.1371/journal.pone.0285576
Abstrakt: Messenger RNA uridylation is pervasive and conserved among eukaryotes, but the consequences of this modification for mRNA fate are still under debate. Utilising a simple model organism to study uridylation may facilitate efforts to understand the cellular function of this process. Here we demonstrate that uridylation can be detected using simple bioinformatics approach. We utilise it to unravel widespread transcript uridylation in fission yeast and demonstrate the contribution of both Cid1 and Cid16, the only two annotated terminal uridyltransferases (TUT-ases) in this yeast. To detect uridylation in transcriptome data, we used a RNA-sequencing (RNA-seq) library preparation protocol involving initial linker ligation to fragmented RNA-an approach borrowed from small RNA sequencing that was commonly used in older RNA-seq protocols. We next explored the data to detect uridylation marks. Our analysis show that uridylation in yeast is pervasive, similarly to the one in multicellular organisms. Importantly, our results confirm the role of the cytoplasmic uridyltransferase Cid1 as the primary uridylation catalyst. However, we also observed an auxiliary role of the second uridyltransferase, Cid16. Thus both fission yeast uridyltransferases are involved in mRNA uridylation. Intriguingly, we found no physiological phenotype of the single and double deletion mutants of cid1 and cid16 and only minimal impact of uridylation on steady-state mRNA levels. Our work establishes fission yeast as a potent model to study uridylation in a simple eukaryote, and we demonstrate that it is possible to detect uridylation marks in RNA-seq data without the need for specific methodologies.
Competing Interests: the authors have declared that no competing interests exist.
(Copyright: © 2023 Lipińska-Zubrycka et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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