ArticleCurrent genetics2020
Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality.
Article in Current genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 22 citations in OpenAlex.
- Transposon-based genome editing of industrial microorganisms: advances, challenges, and prospects.Synthetic and systems biotechnology · 2026Review
- Facile generation ofMicrobiology spectrum · 2026Article
- Predicting FOX gene candidates for oxic nitrogen fixation using multi-omic machine learning and comparative bioinformatics.Scientific reports · 2026Article
- Integrating yeast biodiversity and machine learning for predictive metabolic engineering.FEMS yeast research · 2025Review
- Transposon-sequencing (Tn-seq) of the Candida glabrata reference strain CBS138 reveals epigenetic plasticity, structural variation, and intrinsic mechanisms of resistance to micafungin.G3 (Bethesda, Md.) · 2024Article
- Copy number variation alters local and global mutational tolerance.Genome research · 2023Article
- Advances in transposable elements: from mechanisms to applications in mammalian genomics.Frontiers in genetics · 2023Review
- Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms.Nature communications · 2022Article
- Genome-wide screens in yeast models towards understanding chronological lifespan regulation.Briefings in functional genomics · 2022Article
- SAturated Transposon Analysis in Yeast (SATAY) for Deep Functional Mapping of Yeast Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Contemporary Transposon Tools: A Review and Guide through Mechanisms and Applications ofInternational journal of molecular sciences · 2021Review
- Hijacking Transposable Elements for Saturation Mutagenesis in Fungi.Frontiers in fungal biology · 2021Review
- Transposon Insertion Sequencing, a Global Measure of Gene Function.Annual review of genetics · 2020Review
- Identification of Essential Genes and Fluconazole Susceptibility Genes inG3 (Bethesda, Md.) · 2020Article
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
In vivo transposon mutagenesis, coupled with deep sequencing, enables large-scale genome-wide mutant screens for genes essential in different growth conditions. We analyzed six large-scale studies performed on haploid strains of three yeast species (Saccharomyces cerevisiae, Schizosaccaromyces pombe, and Candida albicans), each mutagenized with two of three different heterologous transposons (AcDs, Hermes, and PiggyBac). Using a machine-learning approach, we evaluated the ability of the data to predict gene essentiality. Important data features included sufficient numbers and distribution of independent insertion events. All transposons showed some bias in insertion site preference because of jackpot events, and preferences for specific insertion sequences and short-distance vs long-distance insertions. For PiggyBac, a stringent target sequence limited the ability to predict essentiality in genes with few or no target sequences. The machine learning approach also robustly predicted gene function in less well-studied species by leveraging cross-species orthologs. Finally, comparisons of isogenic diploid versus haploid S. cerevisiae isolates identified several genes that are haplo-insufficient, while most essential genes, as expected, were recessive. We provide recommendations for the choice of transposons and the inference of gene essentiality in genome-wide studies of eukaryotic haploid microbes such as yeasts, including species that have been less amenable to classical genetic studies.
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