Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés1,
- Marta Huertas1,
- Simone G. Moro1,
- William R. Blevins1,4,
- Mercè Carmona2,
- José Ayté2,
- Elena Hidalgo2 and
- M. Mar Albà1,3
- 1Evolutionary Genomics Group, Research Program on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain;
- 2Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain;
- 3Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
Abstract
The unicellular yeast Schizosaccharomyces pombe (fission yeast) retains many of the splicing features observed in humans and is thus an excellent model to study the basic mechanisms of splicing. Nearly half the genes contain introns, but the impact of alternative splicing in gene regulation and proteome diversification remains largely unexplored. Here we leverage Oxford Nanopore Technologies native RNA sequencing (dRNA), as well as ribosome profiling data, to uncover the full range of polyadenylated transcripts and translated open reading frames. We identify 332 alternative isoforms affecting the coding sequences of 262 different genes, 97 of which occur at frequencies >20%, indicating that functional alternative splicing in S. pombe is more prevalent than previously suspected. Intron retention events make ∼80% of the cases; these events may be involved in the regulation of gene expression and, in some cases, generate novel protein isoforms, as supported by ribosome profiling data in 18 of the intron retention isoforms. One example is the rpl22 gene, in which intron retention is associated with the translation of a protein of only 13 amino acids. We also find that lowly expressed transcripts tend to have longer poly(A) tails than highly expressed transcripts, highlighting an interdependence between poly(A) tail length and transcript expression level. Finally, we discover 214 novel transcripts that are not annotated, including 158 antisense transcripts, some of which also show translation evidence. The methodologies described in this work open new opportunities to study the regulation of splicing in a simple eukaryotic model.
Footnotes
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↵4 Present address: CNAG-CRG, Centre for Genomic Regulation (CRG), 08028 Barcelona, Spain
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.276516.121.
- Received December 20, 2021.
- Accepted May 9, 2022.
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