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Title: Schizophyllum commune has an extensive and functional alternative splicing repertoire

Abstract

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 exploitedmore » dynamically.« less

Authors:
 [1];  [2];  [2];  [2];  [3];  [1]
  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)
Publication Date:
Research Org.:
Broad Inst. of MIT and Harvard, Cambridge, MA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Netherlands Organisation for Scientific Research (NWO)
OSTI Identifier:
1378479
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Fungal genetics; Gene regulation; Protein function predictions; RNA sequencing; RNA splicing

Citation Formats

Gehrmann, Thies, Pelkmans, Jordi F., Lugones, Luis G., Wösten, Han A. B., Abeel, Thomas, and Reinders, Marcel J. T. Schizophyllum commune has an extensive and functional alternative splicing repertoire. United States: N. p., 2016. Web. doi:10.1038/srep33640.
Gehrmann, Thies, Pelkmans, Jordi F., Lugones, Luis G., Wösten, Han A. B., Abeel, Thomas, & Reinders, Marcel J. T. Schizophyllum commune has an extensive and functional alternative splicing repertoire. United States. doi:10.1038/srep33640.
Gehrmann, Thies, Pelkmans, Jordi F., Lugones, Luis G., Wösten, Han A. B., Abeel, Thomas, and Reinders, Marcel J. T. Fri . "Schizophyllum commune has an extensive and functional alternative splicing repertoire". United States. doi:10.1038/srep33640. https://www.osti.gov/servlets/purl/1378479.
@article{osti_1378479,
title = {Schizophyllum commune has an extensive and functional alternative splicing repertoire},
author = {Gehrmann, Thies and Pelkmans, Jordi F. and Lugones, Luis G. and Wösten, Han A. B. and Abeel, Thomas and Reinders, Marcel J. T.},
abstractNote = {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.},
doi = {10.1038/srep33640},
journal = {Scientific Reports},
number = 1,
volume = 6,
place = {United States},
year = {Fri Sep 23 00:00:00 EDT 2016},
month = {Fri Sep 23 00:00:00 EDT 2016}
}

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Works referenced in this record:

InterProScan - an integration platform for the signature-recognition methods in InterPro
journal, September 2001