title: Intron retention-dependent gene regulation in Cryptococcus neoformans.
abstract: 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.
authors: Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015, Paris, France.
authors: Sara
authors: S
authors: Gonzalez-Hilarion
authors: Institut Pasteur, Plate-forme transcriptome et Epigénome, Département Génomes et Génétique, F-75015, Paris, France.
authors: Damien
authors: D
authors: Paulet
authors: Department of Biotechnology, College of Life and Biotechnology, Yonsei University, Seoul 03722, Korea.
authors: Kyung-Tae
authors: KT
authors: Lee
authors: RIKEN Center for Life Science Technologies, Yokohama Institute, Division of Genomic Technology, Yokohama, 230-0045, Japan.
authors: Chung-Chau
authors: CC
authors: Hon
authors: Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, F-75015, Paris, France.
authors: Pierre
authors: P
authors: Lechat
authors: Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015, Paris, France.
authors: Estelle
authors: E
authors: Mogensen
authors: Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015, Paris, France.
authors: Frédérique
authors: F
authors: Moyrand
authors: Institut Pasteur, Plate-forme transcriptome et Epigénome, Département Génomes et Génétique, F-75015, Paris, France.
authors: Caroline
authors: C
authors: Proux
authors: Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015, Paris, France.
authors: Rony
authors: R
authors: Barboux
authors: Institut Pasteur, HUB Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, F-75015, Paris, France.
authors: Giovanni
authors: G
authors: Bussotti
authors: Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea.
authors: Jungwook
authors: J
authors: Hwang
authors: Institut Pasteur, Plate-forme transcriptome et Epigénome, Département Génomes et Génétique, F-75015, Paris, France.
authors: Jean-Yves
authors: JY
authors: Coppée
authors: Department of Biotechnology, College of Life and Biotechnology, Yonsei University, Seoul 03722, Korea.
authors: Yong-Sun
authors: YS
authors: Bahn
authors: Institut Pasteur, Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, F-75015, Paris, France.
authors: Guilhem
authors: G
authors: Janbon
mesh_terms: D017398:Alternative Splicing; D003455:Cryptococcus neoformans / Q000235:genetics* / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D007438:Introns; D058977:Molecular Sequence Annotation; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D020871:RNA Stability
chemical_list: D005656:Fungal Proteins; D020543:Proteome