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Schizophyllum commune has an extensive and functional alternative splicing repertoire

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...

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Autores principales: Gehrmann, Thies, Pelkmans, Jordi F., Lugones, Luis G., Wösten, Han A. B., Abeel, Thomas, Reinders, Marcel J. T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5034255/
https://www.ncbi.nlm.nih.gov/pubmed/27659065
http://dx.doi.org/10.1038/srep33640
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author Gehrmann, Thies
Pelkmans, Jordi F.
Lugones, Luis G.
Wösten, Han A. B.
Abeel, Thomas
Reinders, Marcel J. T.
author_facet Gehrmann, Thies
Pelkmans, Jordi F.
Lugones, Luis G.
Wösten, Han A. B.
Abeel, Thomas
Reinders, Marcel J. T.
author_sort Gehrmann, Thies
collection PubMed
description 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. 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.
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spelling pubmed-50342552016-09-29 Schizophyllum commune has an extensive and functional alternative splicing repertoire Gehrmann, Thies Pelkmans, Jordi F. Lugones, Luis G. Wösten, Han A. B. Abeel, Thomas Reinders, Marcel J. T. Sci Rep Article 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. 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. Nature Publishing Group 2016-09-23 /pmc/articles/PMC5034255/ /pubmed/27659065 http://dx.doi.org/10.1038/srep33640 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
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
title Schizophyllum commune has an extensive and functional alternative splicing repertoire
title_full Schizophyllum commune has an extensive and functional alternative splicing repertoire
title_fullStr Schizophyllum commune has an extensive and functional alternative splicing repertoire
title_full_unstemmed Schizophyllum commune has an extensive and functional alternative splicing repertoire
title_short Schizophyllum commune has an extensive and functional alternative splicing repertoire
title_sort schizophyllum commune has an extensive and functional alternative splicing repertoire
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5034255/
https://www.ncbi.nlm.nih.gov/pubmed/27659065
http://dx.doi.org/10.1038/srep33640
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