Genome‐wide survey of transcriptional initiation in the pathogenic fungus, Candida glabrata

Aoyama, Toshihiro; Nakayama, Hironobu; Ueno, Keigo; Inukai, Tatsuya; Tanabe, Koichi; Nagi, Minoru; Bard, Martin; Chibana, Hiroji

doi:10.1111/gtc.12147

Cited by 12Fungal and yeast genetics researchGenomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Genome‐wide survey of transcriptional initiation in the pathogenic fungus, Candida glabrata

Aoyama, Toshihiro, Nakayama, Hironobu, Ueno, Keigo, Inukai, Tatsuya, Tanabe, Koichi, Nagi, Minoru, Bard, Martin, Chibana, Hiroji·2014·Genes to Cells

DOI 10.1111/gtc.12147

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Abstract

DNA sequencing of the 5'-flanking region of the transcriptome effectively identifies transcription initiation sites and also aids in identifying unknown genes. This study describes a comprehensive polling of transcription start sites and an analysis of full-length complementary DNAs derived from the genome of the pathogenic fungus Candida glabrata. A comparison of the sequence reads derived from a cDNA library prepared from cells grown under different culture conditions against the reference genomic sequence of the Candida Genome Database (CGD: http://www.candidagenome.org/) revealed the expression of 4316 genes and their acknowledged transcription start sites (TSSs). In addition this analysis also predicted 59 new genes including 22 that showed no homology to the genome of Saccharomyces cerevisiae, a genetically close relative of C. glabrata. Furthermore, comparison of the 5'-untranslated regions (5'-UTRs) and core promoters of C. glabrata to those of S. cerevisiae showed various global similarities and differences among orthologous genes. Thus, the C. glabrata transcriptome can complement the annotation of the genome database and should provide new insights into the organization, regulation, and function of genes of this important human pathogen.

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Aoyama et al. (2014) used RNA-seq to investigate transcriptional initiation in Candida glabrata and predicted 50 new Candida glabrata genes.
“for example, Aoyama et al. (2014) used RNA-seq to investigate transcriptional initiation in C. glabrata and predicted 50 new C. glabrata genes.”
From Candida glabrata : new tools and technologies—expanding the toolkit (2015) · cites this paper as Aoyama et al. 2014
Both Aoyama et al. (2014) and Linde et al. (2015) found divergence in the transcriptional regulation between C. glabrata and S. cerevisiae, reinforcing the idea that great care should be taken when extrapolating such regulatory data between species.
“Interestingly both Aoyama et al. (2014) and Linde et al. (2015) found divergence in the transcriptional regulation between C. glabrata and S. cerevisiae, thereby reinforcing the idea that great care should be taken when extrapolating such regulatory data between species.”
From Candida glabrata : new tools and technologies—expanding the toolkit (2015) · cites this paper as Aoyama et al. 2014
252 genes in S. cerevisiae have been reported to contain upstream small open reading frames (uORFS) that can inhibit translation of the downstream ORF, and none of the C. glabrata orthologous genes were reported to contain uORFs.
“For example, 252 genes in S. cerevisiae have been reported to contain upstream small open reading frames (uORFS) that can inhibit translation of the downstream ORF by interfering with the initiation of translation from its start codon. None of the C. glabrata orthologous genes were reported to contain uORFs (Aoyama et al. 2014).”
From Candida glabrata : new tools and technologies—expanding the toolkit (2015) · cites this paper as Aoyama et al. 2014
Based on CAGE analysis, Aoyama et al. predicted 72 C. glabrata genes to contain uORFs, yet none of the 72 S. cerevisiae orthologues have been reported to harbour uORFs; these data strongly suggest that there is regulatory divergence between these two yeasts.
“Instead, based on the CAGE analysis, Aoyama et al. predicted 72 C. glabrata genes to contain uORFs, yet none of the 72 S. cerevisiae orthologues have been reported to harbour uORFs. These data strongly suggest that there is regulatory divergence between these two yeasts (Aoyama et al. 2014).”
From Candida glabrata : new tools and technologies—expanding the toolkit (2015) · cites this paper as Aoyama et al. 2014
Aoyama et al. performed CAGE analysis on RNA isolated from C. glabrata grown in seven different conditions, and this analysis suggested the existence of more than 50 previously unannotated C. glabrata genes as well as confirming the identity of 4316 genes previously listed on the Candida Genome Database.
“Indeed, recently Aoyama et al. performed Cap Analysis Gene Expression (CAGE analysis), a method that was introduced to determine the transcription start sites on a genome-wide scale by isolating and sequencing fragments originating from the 5′ end of RNA transcripts, on RNA isolated from C. glabrata grown in seven different conditions. This analysis suggested the existence of more than 50”
From Candida glabrata : new tools and technologies—expanding the toolkit (2015) · cites this paper as Aoyama et al. 2014

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Authors: Aoyama, T., Nakayama, H., Ueno, K., Inukai, T., Tanabe, K., Nagi, M., Bard, M., & Chibana, H.
Affiliations: National Institute of Technology, Suzuka College (JP)
Suzuka University of Medical Science (JP)
National Institute of Infectious Diseases (JP)
Indiana University – Purdue University Indianapolis (US)
Medical Mycology Research Center, Chiba University (JP)
Corresponding author: Nakayama, Hironobu
ORCID: Aoyama, Toshihiro
Nakayama, Hironobu
Ueno, Keigo
Inukai, Tatsuya
Tanabe, Koichi
Chibana, Hiroji
Venue: Genes to Cells
Publisher: Wiley
Published: 2014-04-14
Volume: 19
Issue: 6
Pages: 478-503
ISSN: 1356-9597 (ISSN-L)
1365-2443
DOI: 10.1111/gtc.12147
OpenAlex: W2055755434
Cited by: 12
References: 30
Citations by year: 2024: 2 · 2023: 2 · 2022: 3 · 2017: 2 · 2016: 1 · 2015: 2
FWCI: 0.68
Type: journal article
Language: en
Open access: closed
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations: Genes to Cells (publishedVersion)
PubMed (publishedVersion)
Funders: Japan Society for the Promotion of Science (23590502, 26860296, 24790428, 24590540)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: Candida glabrata, transcription start sites, transcription initiation, 5'-flanking region, transcriptome, full-length cDNA, 5' untranslated region, core promoter, genome annotation, fungal gene regulation, human pathogenic fungi
MeSH terms: Promoter Regions, Genetic, Saccharomyces cerevisiae, Genome, Fungal, 5' Untranslated Regions, Gene Expression Profiling, Transcription Initiation Site, Candida glabrata, Transcription Initiation, Genetic, Gene Ontology

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Genome‐wide survey of transcriptional initiation in the pathogenic fungus, Candida glabrata

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