Functional profiling of the Saccharomyces cerevisiae genome

Guri Giaever; Angela M Chu; Li Ni; Carla Connelly; Linda Riles; Steeve Véronneau; Sally Dow; Ankuta Lucau-Danila; Keith Anderson; Bruno André; Adam P Arkin; Anna Astromoff; Mohamed El-Bakkoury; Rhonda Bangham; Rocio Benito; Sophie Brachat; Stefano Campanaro; Matt Curtiss; Karen Davis; Adam Deutschbauer; Karl-Dieter Entian; Patrick Flaherty; Francoise Foury; David J Garfinkel; Mark Gerstein; Deanna Gotte; Ulrich Güldener; Johannes H Hegemann; Svenja Hempel; Zelek Herman; Daniel F Jaramillo; Diane E Kelly; Steven L Kelly; Peter Kötter; Darlene LaBonte; David C Lamb; Ning Lan; Hong Liang; Hong Liao; Lucy Liu; Chuanyun Luo; Marc Lussier; Rong Mao; Patrice Menard; Siew Loon Ooi; Jose L Revuelta; Christopher J Roberts; Matthias Rose; Petra Ross-Macdonald; Bart Scherens; Greg Schimmack; Brenda Shafer; Daniel D Shoemaker; Sharon Sookhai-Mahadeo; Reginald K Storms; Jeffrey N Strathern; Giorgio Valle; Marleen Voet; Guido Volckaert; Ching-yun Wang; Teresa R Ward; Julie Wilhelmy; Elizabeth A Winzeler; Yonghong Yang; Grace Yen; Elaine Youngman; Kexin Yu; Howard Bussey; Jef D Boeke; Michael Snyder; Peter Philippsen; Ronald W Davis; Mark Johnston

doi:10.1038/nature00935

Functional profiling of the Saccharomyces cerevisiae genome

Guri Giaever, Angela M Chu, Li Ni, Carla Connelly, Linda Riles, Steeve Véronneau, Sally Dow, Ankuta Lucau-Danila, Keith Anderson, Bruno André, Adam P Arkin, Anna Astromoff, Mohamed El-Bakkoury, Rhonda Bangham, Rocio Benito, Sophie Brachat, Stefano Campanaro, Matt Curtiss, Karen Davis, Adam DeutschbauerKarl-Dieter Entian, Patrick Flaherty, Francoise Foury, David J Garfinkel, Mark Gerstein, Deanna Gotte, Ulrich Güldener, Johannes H Hegemann, Svenja Hempel, Zelek Herman, Daniel F Jaramillo, Diane E Kelly, Steven L Kelly, Peter Kötter, Darlene LaBonte, David C Lamb, Ning Lan, Hong Liang, Hong Liao, Lucy Liu, Chuanyun Luo, Marc Lussier, Rong Mao, Patrice Menard, Siew Loon Ooi, Jose L Revuelta, Christopher J Roberts, Matthias Rose, Petra Ross-Macdonald, Bart Scherens, Greg Schimmack, Brenda Shafer, Daniel D Shoemaker, Sharon Sookhai-Mahadeo, Reginald K Storms, Jeffrey N Strathern, Giorgio Valle, Marleen Voet, Guido Volckaert, Ching-yun Wang, Teresa R Ward, Julie Wilhelmy, Elizabeth A Winzeler, Yonghong Yang, Grace Yen, Elaine Youngman, Kexin Yu, Howard Bussey, Jef D Boeke, Michael Snyder, Peter Philippsen, Ronald W Davis, Mark Johnston

2967 Citations (Scopus)

Abstract

Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.

Original language	English
Journal	Nature
Volume	418
Issue number	6896
Pages (from-to)	387-91
Number of pages	4
ISSN	0028-0836
DOIs	https://doi.org/10.1038/nature00935
Publication status	Published - 2002
Externally published	Yes

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Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., Arkin, A. P., Astromoff, A., El-Bakkoury, M., Bangham, R., Benito, R., Brachat, S., Campanaro, S., Curtiss, M., Davis, K., ... Johnston, M. (2002). Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418(6896), 387-91. https://doi.org/10.1038/nature00935

Giaever, G, Chu, AM, Ni, L, Connelly, C, Riles, L, Véronneau, S, Dow, S, Lucau-Danila, A, Anderson, K, André, B, Arkin, AP, Astromoff, A, El-Bakkoury, M, Bangham, R, Benito, R, Brachat, S, Campanaro, S, Curtiss, M, Davis, K, Deutschbauer, A, Entian, K-D, Flaherty, P, Foury, F, Garfinkel, DJ, Gerstein, M, Gotte, D, Güldener, U, Hegemann, JH, Hempel, S, Herman, Z, Jaramillo, DF, Kelly, DE, Kelly, SL, Kötter, P, LaBonte, D, Lamb, DC, Lan, N, Liang, H, Liao, H, Liu, L, Luo, C, Lussier, M, Mao, R, Menard, P, Ooi, SL, Revuelta, JL, Roberts, CJ, Rose, M, Ross-Macdonald, P, Scherens, B, Schimmack, G, Shafer, B, Shoemaker, DD, Sookhai-Mahadeo, S, Storms, RK, Strathern, JN, Valle, G, Voet, M, Volckaert, G, Wang, C, Ward, TR, Wilhelmy, J, Winzeler, EA, Yang, Y, Yen, G, Youngman, E, Yu, K, Bussey, H, Boeke, JD, Snyder, M, Philippsen, P, Davis, RW & Johnston, M 2002, 'Functional profiling of the Saccharomyces cerevisiae genome', Nature, vol. 418, no. 6896, pp. 387-91. https://doi.org/10.1038/nature00935

@article{2b9e6ee05da311df928f000ea68e967b,

title = "Functional profiling of the Saccharomyces cerevisiae genome",

abstract = "Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.",

author = "Guri Giaever and Chu, {Angela M} and Li Ni and Carla Connelly and Linda Riles and Steeve V{\'e}ronneau and Sally Dow and Ankuta Lucau-Danila and Keith Anderson and Bruno Andr{\'e} and Arkin, {Adam P} and Anna Astromoff and Mohamed El-Bakkoury and Rhonda Bangham and Rocio Benito and Sophie Brachat and Stefano Campanaro and Matt Curtiss and Karen Davis and Adam Deutschbauer and Karl-Dieter Entian and Patrick Flaherty and Francoise Foury and Garfinkel, {David J} and Mark Gerstein and Deanna Gotte and Ulrich G{\"u}ldener and Hegemann, {Johannes H} and Svenja Hempel and Zelek Herman and Jaramillo, {Daniel F} and Kelly, {Diane E} and Kelly, {Steven L} and Peter K{\"o}tter and Darlene LaBonte and Lamb, {David C} and Ning Lan and Hong Liang and Hong Liao and Lucy Liu and Chuanyun Luo and Marc Lussier and Rong Mao and Patrice Menard and Ooi, {Siew Loon} and Revuelta, {Jose L} and Roberts, {Christopher J} and Matthias Rose and Petra Ross-Macdonald and Bart Scherens and Greg Schimmack and Brenda Shafer and Shoemaker, {Daniel D} and Sharon Sookhai-Mahadeo and Storms, {Reginald K} and Strathern, {Jeffrey N} and Giorgio Valle and Marleen Voet and Guido Volckaert and Ching-yun Wang and Ward, {Teresa R} and Julie Wilhelmy and Winzeler, {Elizabeth A} and Yonghong Yang and Grace Yen and Elaine Youngman and Kexin Yu and Howard Bussey and Boeke, {Jef D} and Michael Snyder and Peter Philippsen and Davis, {Ronald W} and Mark Johnston",

note = "Keywords: Cell Size; Cluster Analysis; Culture Media; Galactose; Gene Deletion; Gene Expression Profiling; Genes, Fungal; Genome, Fungal; Hydrogen-Ion Concentration; Nystatin; Open Reading Frames; Osmolar Concentration; Phenotype; Proteome; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Selection, Genetic; Sorbitol",

year = "2002",

doi = "10.1038/nature00935",

language = "English",

volume = "418",

pages = "387--91",

journal = "Nature",

issn = "0028-0836",

publisher = "nature publishing group",

number = "6896",

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TY - JOUR

T1 - Functional profiling of the Saccharomyces cerevisiae genome

AU - Giaever, Guri

AU - Chu, Angela M

AU - Ni, Li

AU - Connelly, Carla

AU - Riles, Linda

AU - Véronneau, Steeve

AU - Dow, Sally

AU - Lucau-Danila, Ankuta

AU - Anderson, Keith

AU - André, Bruno

AU - Arkin, Adam P

AU - Astromoff, Anna

AU - El-Bakkoury, Mohamed

AU - Bangham, Rhonda

AU - Benito, Rocio

AU - Brachat, Sophie

AU - Campanaro, Stefano

AU - Curtiss, Matt

AU - Davis, Karen

AU - Deutschbauer, Adam

AU - Entian, Karl-Dieter

AU - Flaherty, Patrick

AU - Foury, Francoise

AU - Garfinkel, David J

AU - Gerstein, Mark

AU - Gotte, Deanna

AU - Güldener, Ulrich

AU - Hegemann, Johannes H

AU - Hempel, Svenja

AU - Herman, Zelek

AU - Jaramillo, Daniel F

AU - Kelly, Diane E

AU - Kelly, Steven L

AU - Kötter, Peter

AU - LaBonte, Darlene

AU - Lamb, David C

AU - Lan, Ning

AU - Liang, Hong

AU - Liao, Hong

AU - Liu, Lucy

AU - Luo, Chuanyun

AU - Lussier, Marc

AU - Mao, Rong

AU - Menard, Patrice

AU - Ooi, Siew Loon

AU - Revuelta, Jose L

AU - Roberts, Christopher J

AU - Rose, Matthias

AU - Ross-Macdonald, Petra

AU - Scherens, Bart

AU - Schimmack, Greg

AU - Shafer, Brenda

AU - Shoemaker, Daniel D

AU - Sookhai-Mahadeo, Sharon

AU - Storms, Reginald K

AU - Strathern, Jeffrey N

AU - Valle, Giorgio

AU - Voet, Marleen

AU - Volckaert, Guido

AU - Wang, Ching-yun

AU - Ward, Teresa R

AU - Wilhelmy, Julie

AU - Winzeler, Elizabeth A

AU - Yang, Yonghong

AU - Yen, Grace

AU - Youngman, Elaine

AU - Yu, Kexin

AU - Bussey, Howard

AU - Boeke, Jef D

AU - Snyder, Michael

AU - Philippsen, Peter

AU - Davis, Ronald W

AU - Johnston, Mark

N1 - Keywords: Cell Size; Cluster Analysis; Culture Media; Galactose; Gene Deletion; Gene Expression Profiling; Genes, Fungal; Genome, Fungal; Hydrogen-Ion Concentration; Nystatin; Open Reading Frames; Osmolar Concentration; Phenotype; Proteome; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Selection, Genetic; Sorbitol

PY - 2002

Y1 - 2002

N2 - Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.

AB - Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.

U2 - 10.1038/nature00935

DO - 10.1038/nature00935

M3 - Journal article

C2 - 12140549

SN - 0028-0836

VL - 418

SP - 387

EP - 391

JO - Nature

JF - Nature

IS - 6896

ER -

Functional profiling of the Saccharomyces cerevisiae genome

Abstract

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