Schizophyllum commune has an extensive and functional alternative splicing repertoire

Journal Article · Fri Sep 23 00:00:00 EDT 2016 · Scientific Reports

DOI:https://doi.org/10.1038/srep33640· OSTI ID:1378479

Gehrmann, Thies ^[1]; Pelkmans, Jordi F. ^[2]; Lugones, Luis G. ^[2]; Wösten, Han A. B. ^[2]; Abeel, Thomas ^[3]; Reinders, Marcel J. T. ^[1]

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1. Delft Univ. of Technology (Netherlands). Delft Bioinformatics Lab.
2. Utrecht Univ., Utrecht (The Netherlands). Microbiology Dept. of Biology
3. Delft Univ. of Technology (Netherlands). Delft Bioinformatics Lab.; Broad Inst. of MIT and Harvard, Cambridge, MA (United States)

Recent genome-wide studies have demonstrated that fungi possess the machinery to alternatively splice pre-mRNA. However, there has not been a systematic categorization of the functional impact of alternative splicing in a fungus. We investigate alternative splicing and its functional consequences in the model mushroom forming fungus Schizophyllum commune. Alternative splicing was demonstrated for 2,285 out of 12,988 expressed genes, resulting in 20% additional transcripts. Intron retentions were the most common alternative splicing events, accounting for 33% of all splicing events, and 43% of the events in coding regions. On the other hand, exon skipping events were rare in coding regions (1%) but enriched in UTRs where they accounted for 57% of the events. Specific functional groups, including transcription factors, contained alternatively spliced genes. Alternatively spliced transcripts were regulated differently throughout development in 19% of the 2,285 alternatively spliced genes. Notably, 69% of alternatively spliced genes have predicted alternative functionality by loss or gain of functional domains, or by acquiring alternative subcellular locations. S. commune exhibits more alternative splicing than any other studied fungus. Finally, taken together, alternative splicing increases the complexity of the S. commune proteome considerably and provides it with a rich repertoire of alternative functionality that is exploited dynamically.

• Research Organization: Broad Inst. of MIT and Harvard, Cambridge, MA (United States)
• Sponsoring Organization: USDOE Office of Science (SC); Netherlands Organisation for Scientific Research (NWO)
• OSTI ID: 1378479
• Journal Information: Scientific Reports, Vol. 6, Issue 1; ISSN 2045-2322
• Publisher: Nature Publishing Group
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Fungal genetics
Gene regulation
Protein function predictions
RNA sequencing
RNA splicing