Functional mapping of yeast genomes by saturated transposition

Agnès H Michel; Riko Hatakeyama; Philipp Kimmig; Meret Arter; Matthias Peter; Joao Matos; Claudio De Virgilio; Benoît Kornmann

doi:10.7554/eLife.23570

Functional mapping of yeast genomes by saturated transposition

Agnès H Michel, Riko Hatakeyama, Philipp Kimmig, Meret Arter, Matthias Peter, Joao Matos, Claudio De Virgilio, Benoît Kornmann^* (Corresponding Author)

^*Corresponding author for this work

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Abstract

Yeast is a powerful model for systems genetics. We present a versatile, time- and labor-efficient method to functionally explore the Saccharomyces cerevisiae genome using saturated transposon mutagenesis coupled to high-throughput sequencing. SAturated Transposon Analysis in Yeast (SATAY) allows one-step mapping of all genetic loci in which transposons can insert without disrupting essential functions. SATAY is particularly suited to discover loci important for growth under various conditions. SATAY (1) reveals positive and negative genetic interactions in single and multiple mutant strains, (2) can identify drug targets, (3) detects not only essential genes, but also essential protein domains, (4) generates both null and other informative alleles. In a SATAY screen for rapamycin-resistant mutants, we identify Pib2 (PhosphoInositide-Binding 2) as a master regulator of TORC1. We describe two antagonistic TORC1-activating and -inhibiting activities located on opposite ends of Pib2. Thus, SATAY allows to easily explore the yeast genome at unprecedented resolution and throughput.

Original language	English
Article number	e23570
Number of pages	28
Journal	eLife
Volume	6
Early online date	8 May 2017
DOIs	https://doi.org/10.7554/eLife.23570
Publication status	Published - 9 Jun 2017
Externally published	Yes

Bibliographical note

Acknowledgements
We thank Beat Christen for inspiring this work and expert insight on Tn-seq, Reinhard Kunze for kind gift of plasmid and strain, Asun Monfort Pineda and Anton Wutz for invaluable help with Illumina Sequencing, Jeremy Thorner, Karsten Weis, Jeffrey Tang, Judith Berman and Vladimir Gritsenko for helpful discussions, Christine Doderer for preliminary experiments, Alicia Smith for comments on the manuscript, and the Kornmann lab for comments and ideas. This work is supported by grants of the Swiss National Science Foundation (PP00P3_13365 to BK, 310030_166474 to CDV, 31003A_153058 and 155823 to JM), the European Research Council (337906-OrgaNet) to BK, and PK is supported by the Human Frontier Science Program Organization

Keywords

DNA Transposable Elements
Genes, Fungal
Genetics, Microbial/methods
Genome, Fungal
Molecular Sequence Annotation/methods
Mutagenesis, Insertional/methods
Saccharomyces cerevisiae/genetics
Sequence Analysis, DNA

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Riko Hatakeyama
Person: Academic

Cite this

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abstract = "Yeast is a powerful model for systems genetics. We present a versatile, time- and labor-efficient method to functionally explore the Saccharomyces cerevisiae genome using saturated transposon mutagenesis coupled to high-throughput sequencing. SAturated Transposon Analysis in Yeast (SATAY) allows one-step mapping of all genetic loci in which transposons can insert without disrupting essential functions. SATAY is particularly suited to discover loci important for growth under various conditions. SATAY (1) reveals positive and negative genetic interactions in single and multiple mutant strains, (2) can identify drug targets, (3) detects not only essential genes, but also essential protein domains, (4) generates both null and other informative alleles. In a SATAY screen for rapamycin-resistant mutants, we identify Pib2 (PhosphoInositide-Binding 2) as a master regulator of TORC1. We describe two antagonistic TORC1-activating and -inhibiting activities located on opposite ends of Pib2. Thus, SATAY allows to easily explore the yeast genome at unprecedented resolution and throughput.",

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note = "Acknowledgements We thank Beat Christen for inspiring this work and expert insight on Tn-seq, Reinhard Kunze for kind gift of plasmid and strain, Asun Monfort Pineda and Anton Wutz for invaluable help with Illumina Sequencing, Jeremy Thorner, Karsten Weis, Jeffrey Tang, Judith Berman and Vladimir Gritsenko for helpful discussions, Christine Doderer for preliminary experiments, Alicia Smith for comments on the manuscript, and the Kornmann lab for comments and ideas. This work is supported by grants of the Swiss National Science Foundation (PP00P3_13365 to BK, 310030_166474 to CDV, 31003A_153058 and 155823 to JM), the European Research Council (337906-OrgaNet) to BK, and PK is supported by the Human Frontier Science Program Organization",

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AU - Matos, Joao

AU - De Virgilio, Claudio

AU - Kornmann, Benoît

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N2 - Yeast is a powerful model for systems genetics. We present a versatile, time- and labor-efficient method to functionally explore the Saccharomyces cerevisiae genome using saturated transposon mutagenesis coupled to high-throughput sequencing. SAturated Transposon Analysis in Yeast (SATAY) allows one-step mapping of all genetic loci in which transposons can insert without disrupting essential functions. SATAY is particularly suited to discover loci important for growth under various conditions. SATAY (1) reveals positive and negative genetic interactions in single and multiple mutant strains, (2) can identify drug targets, (3) detects not only essential genes, but also essential protein domains, (4) generates both null and other informative alleles. In a SATAY screen for rapamycin-resistant mutants, we identify Pib2 (PhosphoInositide-Binding 2) as a master regulator of TORC1. We describe two antagonistic TORC1-activating and -inhibiting activities located on opposite ends of Pib2. Thus, SATAY allows to easily explore the yeast genome at unprecedented resolution and throughput.

AB - Yeast is a powerful model for systems genetics. We present a versatile, time- and labor-efficient method to functionally explore the Saccharomyces cerevisiae genome using saturated transposon mutagenesis coupled to high-throughput sequencing. SAturated Transposon Analysis in Yeast (SATAY) allows one-step mapping of all genetic loci in which transposons can insert without disrupting essential functions. SATAY is particularly suited to discover loci important for growth under various conditions. SATAY (1) reveals positive and negative genetic interactions in single and multiple mutant strains, (2) can identify drug targets, (3) detects not only essential genes, but also essential protein domains, (4) generates both null and other informative alleles. In a SATAY screen for rapamycin-resistant mutants, we identify Pib2 (PhosphoInositide-Binding 2) as a master regulator of TORC1. We describe two antagonistic TORC1-activating and -inhibiting activities located on opposite ends of Pib2. Thus, SATAY allows to easily explore the yeast genome at unprecedented resolution and throughput.

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KW - Genes, Fungal

KW - Genetics, Microbial/methods

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KW - Molecular Sequence Annotation/methods

KW - Mutagenesis, Insertional/methods

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KW - Sequence Analysis, DNA

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VL - 6

JO - eLife

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M1 - e23570

ER -

Functional mapping of yeast genomes by saturated transposition

Abstract

Bibliographical note

Keywords

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Riko Hatakeyama

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