ArticlePloS one2012
A novel strategy for selection and validation of reference genes in dynamic multidimensional experimental design in yeast.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
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- A high copy suppressor screen identifies factors enhancing the allotopic production of subunit II of cytochrome c oxidase.G3 (Bethesda, Md.) · 2025Article
- Identification of stable reference genes for qRT-PCR in Stropharia rugosoannulata using mRNA-sequencing data.PloS one · 2025Article
- Transcriptional response of Saccharomyces cerevisiae to lactic acid enantiomers.Applied microbiology and biotechnology · 2024Article
- Evaluation of Reference Gene Stability in Goat Skeletal Muscle Satellite Cells during Proliferation and Differentiation Phases.Animals : an open access journal from MDPI · 2024Article
- The influence of self-cycling fermentation long- and short-cycle schemes on Saccharomyces cerevisiae and Escherichia coli.Scientific reports · 2022Article
- SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes.Nature communications · 2022Article
- Transcription-replication coordination revealed in single live cells.Nucleic acids research · 2022Article
- Differential translation elongation directs protein synthesis in response to acute glucose deprivation in yeast.RNA biology · 2022Article
- Transcriptomic analysis of synchrony and productivity in self-cycling fermentation of engineered yeast producing shikimic acid.Biotechnology reports (Amsterdam, Netherlands) · 2021Article
- Glycolytic flux inThe Biochemical journal · 2019Article
- Selection of reference genes for quantitative real-time PCR normalization in the plant pathogen Puccinia helianthi Schw.BMC plant biology · 2019Article
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- Doxorubicin induces an extensive transcriptional and metabolic rewiring in yeast cells.Scientific reports · 2018Article
- Design of RNA hairpin modules that predictably tune translation in yeast.Synthetic biology (Oxford, England) · 2018Article
- Significance of oxygen transport through aquaporins.Scientific reports · 2017Article
- Transcriptomic response of yeast cells to ATX1 deletion under different copper levels.BMC genomics · 2016Article
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- The effect of immunological status, in-vitro treatment and culture time on expression of eleven candidate reference genes in bovine blood mononuclear cells.BMC immunology · 2015Article
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6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundUnderstanding the dynamic mechanism behind the transcriptional organization of genes in response to varying environmental conditions requires time-dependent data. The dynamic transcriptional response obtained by real-time RT-qPCR experiments could only be correctly interpreted if suitable reference genes are used in the analysis. The lack of available studies on the identification of candidate reference genes in dynamic gene expression studies necessitates the identification and the verification of a suitable gene set for the analysis of transient gene expression response. PRINCIPAL
findingsIn this study, a candidate reference gene set for RT-qPCR analysis of dynamic transcriptional changes in Saccharomyces cerevisiae was determined using 31 different publicly available time series transcriptome datasets. Ten of the twelve candidates (TPI1, FBA1, CCW12, CDC19, ADH1, PGK1, GCN4, PDC1, RPS26A and ARF1) we identified were not previously reported as potential reference genes. Our method also identified the commonly used reference genes ACT1 and TDH3. The most stable reference genes from this pool were determined as TPI1, FBA1, CDC19 and ACT1 in response to a perturbation in the amount of available glucose and as FBA1, TDH3, CCW12 and ACT1 in response to a perturbation in the amount of available ammonium. The use of these newly proposed gene sets outperformed the use of common reference genes in the determination of dynamic transcriptional response of the target genes, HAP4 and MEP2, in response to relaxation from glucose and ammonium limitations, respectively.
conclusionsA candidate reference gene set to be used in dynamic real-time RT-qPCR expression profiling in yeast was proposed for the first time in the present study. Suitable pools of stable reference genes to be used under different experimental conditions could be selected from this candidate set in order to successfully determine the expression profiles for the genes of interest.
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