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Genes 2018, 9(3), 118; https://doi.org/10.3390/genes9030118

Genome-Wide Identification of circRNAs in Pathogenic Basidiomycetous Yeast Cryptococcus neoformans Suggests Conserved circRNA Host Genes over Kingdoms

Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, Institute of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University (CLS-BNU), Beijing 100875, China
These authors contributed equally to this work.
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Received: 9 January 2018 / Revised: 9 February 2018 / Accepted: 19 February 2018 / Published: 26 February 2018
(This article belongs to the Special Issue Fungal Pathogenesis in Humans: The Growing Threat)
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Abstract

Circular RNAs (circRNAs), a novel class of ubiquitous and intriguing noncoding RNA, have been found in a number of eukaryotes but not yet basidiomycetes. In this study, we identified 73 circRNAs from 39.28 million filtered RNA reads from the basidiomycete Cryptococcus neoformans JEC21 using next-generation sequencing (NGS) and the bioinformatics tool circular RNA identification (CIRI). Furthermore, mapping of newly found circRNAs to the genome showed that 73.97% of the circRNAs originated from exonic regions, whereas 20.55% were from intergenic regions and 5.48% were from intronic regions. Enrichment analysis of circRNA host genes was conducted based on the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway databases. The results reveal that host genes are mainly responsible for primary metabolism and, interestingly, ribosomal protein production. Furthermore, we uncovered a high-level circRNA that was a transcript from the guanosine triphosphate (GTP)ase gene CNM01190 (gene ID: 3255052) in our yeast. Coincidentally, YPT5, CNM01190′s ortholog of the GTPase in Schizosaccharomyces pombe, protists, and humans, has already been proven to generate circRNAs. Additionally, overexpression of RNA debranching enzyme DBR1 had varied influence on the expression of circRNAs, indicating that multiple circRNA biosynthesis pathways exist in C. neoformans. Our study provides evidence for the existence of stable circRNAs in the opportunistic human pathogen C. neoformans and raises a question regarding their role related to pathogenesis in this yeast. View Full-Text
Keywords: Cryptococcus neoformans; next-generation sequencing (NGS); circRNAs; RNA debranching enzyme; GTPase-encoding gene Cryptococcus neoformans; next-generation sequencing (NGS); circRNAs; RNA debranching enzyme; GTPase-encoding gene
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Huo, L.; Zhang, P.; Li, C.; Rahim, K.; Hao, X.; Xiang, B.; Zhu, X. Genome-Wide Identification of circRNAs in Pathogenic Basidiomycetous Yeast Cryptococcus neoformans Suggests Conserved circRNA Host Genes over Kingdoms. Genes 2018, 9, 118.

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