Intron retention-dependent gene regulation in Cryptococcus neoformans
| Autor: | Estelle Mogensen, Guilhem Janbon, Jungwook Hwang, Rony Barboux, Chung-Chau Hon, Pierre Lechat, Sara Gonzalez-Hilarion, Giovanni Bussotti, Kyung-Tae Lee, Damien Paulet, Jean Yves Coppée, Yong Sun Bahn, Caroline Proux, Frédérique Moyrand |
|---|---|
| Přispěvatelé: | Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris], Transcriptome et Epigénome (PF2), College of Life and Biotechnology [Séoul], Yonsei University, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Hanyang University, This work was supported by National Research Foundation of Korea grants (2015R1A2A1A15055687) from MEST, the Strategic Initiative for Microbiomes in Agriculture and Food funded by Ministry of Agriculture, Food and Rural Affairs (916006-2) (to Y.S.B). This work was supported by a grant from ANR (2010-BLAN-1620-01 program YeastIntrons) to GJ. We thank Tae-Yup Kim and Anna Floyd for their technical assistance. We thank Cecelia Shertz Wall for editing the manuscript., ANR-10-BLAN-1620,YeastIntrons,Analyse globale de la régulation des ARN contenant des PTC par la voie du NMD et le complexe EJC-like chez des levures riches ou pauvres en introns(2010), Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS) |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
MESH: Proteome / metabolism MESH: Gene Expression Proteome RNA Stability 030106 microbiology MESH: Proteome / genetics Gene Expression MESH: Gene Expression Regulation Fungal MESH: Molecular Sequence Annotation Article Fungal Proteins 03 medical and health sciences MESH: Introns Fungal genetics Gene Expression Regulation Fungal Gene expression MESH: Fungal Proteins / genetics Gene MESH: Cryptococcus neoformans / genetics [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology Cryptococcus neoformans Genetics Regulation of gene expression Fungal protein Multidisciplinary biology MESH: Alternative Splicing Alternative splicing Intron MESH: RNA Stability Molecular Sequence Annotation biology.organism_classification Introns Alternative Splicing 030104 developmental biology MESH: Genome Fungal MESH: Cryptococcus neoformans / metabolism MESH: Fungal Proteins / metabolism [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] Genome Fungal |
| Zdroj: | Scientific Reports Scientific Reports, Nature Publishing Group, 2016, 6 (1), pp.32252. ⟨10.1038/srep32252⟩ Scientific Reports, 2016, 6 (1), pp.32252. ⟨10.1038/srep32252⟩ |
| ISSN: | 2045-2322 |
| Popis: | The biological impact of alternative splicing is poorly understood in fungi, although recent studies have shown that these microorganisms are usually intron-rich. In this study, we re-annotated the genome of C. neoformans var. neoformans using RNA-Seq data. Comparison with C. neoformans var. grubii revealed that more than 99% of ORF-introns are in the same exact position in the two varieties whereas UTR-introns are much less evolutionary conserved. We also confirmed that alternative splicing is very common in C. neoformans, affecting nearly all expressed genes. We also observed specific regulation of alternative splicing by environmental cues in this yeast. However, alternative splicing does not appear to be an efficient method to diversify the C. neoformans proteome. Instead, our data suggest the existence of an intron retention-dependent mechanism of gene expression regulation that is not dependent on NMD. This regulatory process represents an additional layer of gene expression regulation in fungi and provides a mechanism to tune gene expression levels in response to any environmental modification. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|