Intron retention-dependent gene regulation in Cryptococcus neoformans.
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ABSTRACT:
SUBMITTER: Gonzalez-Hilarion S
PROVIDER: S-EPMC5006051 | biostudies-literature | 2016 Aug
REPOSITORIES: biostudies-literature
Publications
Intron retention-dependent gene regulation in Cryptococcus neoformans.
Gonzalez-Hilarion Sara S Paulet Damien D Lee Kyung-Tae KT Hon Chung-Chau CC Lechat Pierre P Mogensen Estelle E Moyrand Frédérique F Proux Caroline C Barboux Rony R Bussotti Giovanni G Hwang Jungwook J Coppée Jean-Yves JY Bahn Yong-Sun YS Janbon Guilhem G
Scientific reports 20160831
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 ...[more]
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Project description:Most Cryptococccus neoformans genes are interrupted by introns, and alternative splicing occurs very often. In this study, we examined the influence of introns on C. neoformans gene expression. For most tested genes, elimination of introns greatly reduces mRNA accumulation. Strikingly, the number and the position of introns modulate the gene expression level in a cumulative manner. A screen for mutant strains able to express functionally an intronless allele revealed that the nuclear poly(A) binding protein Pab2 modulates intron-dependent regulation of gene expression in C. neoformans. PAB2 deletion partially restored accumulation of intronless mRNA. In addition, our results demonstrated that the essential nucleases Rrp44p and Xrn2p are implicated in the degradation of mRNA transcribed from an intronless allele in C. neoformans. Double mutant constructions and over-expression experiments suggested that Pab2p and Xrn2p could act in the same pathway whereas Rrp44p appears to act independently. Finally, deletion of the RRP6 or the CID14 gene, encoding the nuclear exosome nuclease and the TRAMP complex associated poly(A) polymerase, respectively, has no effect on intronless allele expression.
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