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

Genes
Liang HuoXudong Zhu

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 basidiomyceteCryptococcus neoformansJEC21 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 geneCNM01190(gene ID: 3255052) in our yeast. Coincidentally,YPT5,CNM01190's ortholog of the GTPase inSchizosaccharomyces pombe, protists, and humans, has already been proven to generate circRNAs. Additionally, overexpression of RNA debranching enzymeDBR1had varied ...Continue Reading

References

Nov 1, 1976·Proceedings of the National Academy of Sciences of the United States of America·H L SangerA K Kleinschmidt
Jun 26, 2003·Nucleic Acids Research·Michael Zuker
Apr 29, 2008·Nucleic Acids Research·Mark JohnsonThomas L Madden
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Oct 13, 2011·Molecular Systems Biology·Fabian SieversDesmond G Higgins
Feb 19, 2013·Cell·Phillip A DumesicHiten D Madhani
Mar 1, 2013·Nature·Thomas B HansenJørgen Kjems
Jun 12, 2013·Fungal Genetics and Biology : FG & B·Elizabeth Ripley BallouJ Andrew Alspaugh
Sep 17, 2013·Molecular Cell·Yang ZhangLing-Ling Chen
Mar 13, 2014·PloS One·Peter L WangJulia Salzman
May 9, 2014·Nature Biotechnology·William R Jeck, Norman E Sharpless
Sep 23, 2014·Molecular Cell·Reut Ashwal-FlussSebastian Kadener
Sep 23, 2014·Cell·Xiao-Ou ZhangLi Yang
Oct 5, 2014·Genes & Development·Dongming Liang, Jeremy E Wilusz
Nov 19, 2014·RNA·Erika Lasda, Roy Parker
Mar 10, 2015·RNA Biology·Ling-Ling Chen, Li Yang
Mar 15, 2015·Cell·Simon J ConnGregory J Goodall
Jul 25, 2015·The New Phytologist·Chu-Yu YeLongjiang Fan
Feb 26, 2016·Nature Reviews. Molecular Cell Biology·Ling-Ling Chen
Apr 7, 2016·Trends in Genetics : TIG·Julia Salzman
Jul 28, 2016·Biochimica Et Biophysica Acta·Javier T Granados-Riveron, Guillermo Aquino-Jarquin
Nov 24, 2016·FEBS Letters·Yudong ShenWeimin Wang
Mar 11, 2017·Molecular Cancer·Jing LiuAili He

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
electrophoresis
reverse transcription PCR
GTPase
RNA-seq

Software Mentioned

Burrows aligner ( BWA )
CIRI
Ensemble
IlluQC
circRNA
Clustal Omega
BLAST ) search
KNIFE
KOBAS
BLAST

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.