The dynamic landscape of fission yeast meiosis alternative-splice isoforms

Zheng Kuang, Jef D. Boeke, Stefan Canzar

Research output: Contribution to journalArticle

Abstract

Alternative splicing increases the diversity of transcriptomes and proteomes in metazoans. The extent to which alternative splicing is active and functional in unicellular organisms is less understood. Here, we exploit a single-molecule long-read sequencing technique and develop an open-source software program called SpliceHunter to characterize the transcriptome in the meiosis of fission yeast. We reveal 14,353 alternative splicing events in 17,669 novel isoforms at different stages of meiosis, including antisense and read-through transcripts. Intron retention is the major type of alternative splicing, followed by alternate "intron in exon." Seven hundred seventy novel transcription units are detected; 53 of the predicted proteins show homology in other species and form theoretical stable structures. We report the complexity of alternative splicing along isoforms, including 683 intra-molecularly co-associated intron pairs. We compare the dynamics of novel isoforms based on the number of supporting full-length reads with those of annotated isoforms and explore the translational capacity and quality of novel isoforms. The evaluation of these factors indicates that the majority of novel isoforms are unlikely to be both condition-specific and translatable but consistent with the possibility of biologically functional novel isoforms. Moreover, the co-option of these unusual transcripts into newly born genes seems likely. Together, the results of this study highlight the diversity and dynamics at the isoform level in the sexual development of fission yeast.

Original languageEnglish (US)
Pages (from-to)145-156
Number of pages12
JournalGenome Research
Volume27
Issue number1
DOIs
StatePublished - Jan 1 2017
Externally publishedYes

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Schizosaccharomyces
Meiosis
Protein Isoforms
Alternative Splicing
Introns
Transcriptome
Sexual Development
Proteome
Exons
Software

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

The dynamic landscape of fission yeast meiosis alternative-splice isoforms. / Kuang, Zheng; Boeke, Jef D.; Canzar, Stefan.

In: Genome Research, Vol. 27, No. 1, 01.01.2017, p. 145-156.

Research output: Contribution to journalArticle

Kuang, Zheng ; Boeke, Jef D. ; Canzar, Stefan. / The dynamic landscape of fission yeast meiosis alternative-splice isoforms. In: Genome Research. 2017 ; Vol. 27, No. 1. pp. 145-156.
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