Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

Dong Uk Kim; Jacqueline Hayles; Dongsup Kim; Valerie Wood; Han Oh Park; Misun Won; Hyang Sook Yoo; Trevor Duhig; Miyoung Nam; Georgia Palmer; Sangjo Han; Linda Jeffery; Seung Tae Baek; Hyemi Lee; Young Sam Shim; Minho Lee; Lila Kim; Kyung Sun Heo; Eun Joo Noh; Ah Reum Lee; Young Joo Jang; Kyung Sook Chung; Shin Jung Choi; Jo Young Park; Youngwoo Park; Hwan Mook Kim; Song Kyu Park; Hae Joon Park; Eun Jung Kang; Hyong Bai Kim; Hyun Sam Kang; Hee Moon Park; Kyunghoon Kim; Kiwon Song; Kyung Bin Song; Paul Nurse; Kwang Lae Hoe

doi:10.1038/nbt.1628

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

Dong Uk Kim, Jacqueline Hayles, Dongsup Kim, Valerie Wood, Han Oh Park, Misun Won, Hyang Sook Yoo, Trevor Duhig, Miyoung Nam, Georgia Palmer, Sangjo Han, Linda Jeffery, Seung Tae Baek, Hyemi Lee, Young Sam Shim, Minho Lee, Lila Kim, Kyung Sun Heo, Eun Joo Noh, Ah Reum LeeYoung Joo Jang, Kyung Sook Chung, Shin Jung Choi, Jo Young Park, Youngwoo Park, Hwan Mook Kim, Song Kyu Park, Hae Joon Park, Eun Jung Kang, Hyong Bai Kim, Hyun Sam Kang, Hee Moon Park, Kyunghoon Kim, Kiwon Song, Kyung Bin Song, Paul Nurse, Kwang Lae Hoe

Research output: Contribution to journal › Article › peer-review

542 Citations (Scopus)

Abstract

We report the construction and analysis of 4,836 heterozygous diploid deletion mutants covering 98.4% of the fission yeast genome providing a tool for studying eukaryotic biology. Comprehensive gene dispensability comparisons with budding yeastthe only other eukaryote for which a comprehensive knockout library existsrevealed that 83% of single-copy orthologs in the two yeasts had conserved dispensability. Gene dispensability differed for certain pathways between the two yeasts, including mitochondrial translation and cell cycle checkpoint control. We show that fission yeast has more essential genes than budding yeast and that essential genes are more likely than nonessential genes to be present in a single copy, to be broadly conserved and to contain introns. Growth fitness analyses determined sets of haploinsufficient and haploproficient genes for fission yeast, and comparisons with budding yeast identified specific ribosomal proteins and RNA polymerase subunits, which may act more generally to regulate eukaryotic cell growth.

Original language	English
Pages (from-to)	617-623
Number of pages	7
Journal	Nature Biotechnology
Volume	28
Issue number	6
DOIs	https://doi.org/10.1038/nbt.1628
Publication status	Published - 2010 Jun

Bibliographical note

Funding Information:
Y.-D. Kim, S. Park, H.-J. Lee, J.-H. Ahn, Y.-S. Kil, S.-Y. Park, J.-H. Lim, J.-H. Song, Y.-K. Ryoo, J.-Y. Kim, M.-J. Oh, S. Kong, J. Ahn, N. Sun, N. Peat, R. Mandeville and J.-J. Li. We also thank J.-H. Roe and W.-K. Huh for reading this manuscript and for their insightful comments and O. Nielsen for his patience with the many requests for pON177. This work was supported by the intramural research program of KRIBB (Mission 2007), the Chemical Genomics Research Program and the 21st Century Frontier Research Program from the Ministry of Education, Science and Technology (MOEST) of Korea. This work was also supported by Bioneer Corp., The Wellcome Trust, Cancer Research UK, The Breast Cancer Research Foundation (BCRF) and The Rockefeller University.

All Science Journal Classification (ASJC) codes

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Molecular Medicine
Biomedical Engineering

Access to Document

10.1038/nbt.1628

Cite this

Kim, D. U., Hayles, J., Kim, D., Wood, V., Park, H. O., Won, M., Yoo, H. S., Duhig, T., Nam, M., Palmer, G., Han, S., Jeffery, L., Baek, S. T., Lee, H., Shim, Y. S., Lee, M., Kim, L., Heo, K. S., Noh, E. J., ... Hoe, K. L. (2010). Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nature Biotechnology, 28(6), 617-623. https://doi.org/10.1038/nbt.1628

@article{7f03afd1042040d8acd882c822ad9c5d,

title = "Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe",

abstract = "We report the construction and analysis of 4,836 heterozygous diploid deletion mutants covering 98.4% of the fission yeast genome providing a tool for studying eukaryotic biology. Comprehensive gene dispensability comparisons with budding yeastthe only other eukaryote for which a comprehensive knockout library existsrevealed that 83% of single-copy orthologs in the two yeasts had conserved dispensability. Gene dispensability differed for certain pathways between the two yeasts, including mitochondrial translation and cell cycle checkpoint control. We show that fission yeast has more essential genes than budding yeast and that essential genes are more likely than nonessential genes to be present in a single copy, to be broadly conserved and to contain introns. Growth fitness analyses determined sets of haploinsufficient and haploproficient genes for fission yeast, and comparisons with budding yeast identified specific ribosomal proteins and RNA polymerase subunits, which may act more generally to regulate eukaryotic cell growth.",

author = "Kim, {Dong Uk} and Jacqueline Hayles and Dongsup Kim and Valerie Wood and Park, {Han Oh} and Misun Won and Yoo, {Hyang Sook} and Trevor Duhig and Miyoung Nam and Georgia Palmer and Sangjo Han and Linda Jeffery and Baek, {Seung Tae} and Hyemi Lee and Shim, {Young Sam} and Minho Lee and Lila Kim and Heo, {Kyung Sun} and Noh, {Eun Joo} and Lee, {Ah Reum} and Jang, {Young Joo} and Chung, {Kyung Sook} and Choi, {Shin Jung} and Park, {Jo Young} and Youngwoo Park and Kim, {Hwan Mook} and Park, {Song Kyu} and Park, {Hae Joon} and Kang, {Eun Jung} and Kim, {Hyong Bai} and Kang, {Hyun Sam} and Park, {Hee Moon} and Kyunghoon Kim and Kiwon Song and Song, {Kyung Bin} and Paul Nurse and Hoe, {Kwang Lae}",

note = "Funding Information: Y.-D. Kim, S. Park, H.-J. Lee, J.-H. Ahn, Y.-S. Kil, S.-Y. Park, J.-H. Lim, J.-H. Song, Y.-K. Ryoo, J.-Y. Kim, M.-J. Oh, S. Kong, J. Ahn, N. Sun, N. Peat, R. Mandeville and J.-J. Li. We also thank J.-H. Roe and W.-K. Huh for reading this manuscript and for their insightful comments and O. Nielsen for his patience with the many requests for pON177. This work was supported by the intramural research program of KRIBB (Mission 2007), the Chemical Genomics Research Program and the 21st Century Frontier Research Program from the Ministry of Education, Science and Technology (MOEST) of Korea. This work was also supported by Bioneer Corp., The Wellcome Trust, Cancer Research UK, The Breast Cancer Research Foundation (BCRF) and The Rockefeller University.",

year = "2010",

month = jun,

doi = "10.1038/nbt.1628",

language = "English",

volume = "28",

pages = "617--623",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

number = "6",

}

Kim, DU, Hayles, J, Kim, D, Wood, V, Park, HO, Won, M, Yoo, HS, Duhig, T, Nam, M, Palmer, G, Han, S, Jeffery, L, Baek, ST, Lee, H, Shim, YS, Lee, M, Kim, L, Heo, KS, Noh, EJ, Lee, AR, Jang, YJ, Chung, KS, Choi, SJ, Park, JY, Park, Y, Kim, HM, Park, SK, Park, HJ, Kang, EJ, Kim, HB, Kang, HS, Park, HM, Kim, K, Song, K, Song, KB, Nurse, P & Hoe, KL 2010, 'Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe', Nature Biotechnology, vol. 28, no. 6, pp. 617-623. https://doi.org/10.1038/nbt.1628

TY - JOUR

T1 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

AU - Kim, Dong Uk

AU - Hayles, Jacqueline

AU - Kim, Dongsup

AU - Wood, Valerie

AU - Park, Han Oh

AU - Won, Misun

AU - Yoo, Hyang Sook

AU - Duhig, Trevor

AU - Nam, Miyoung

AU - Palmer, Georgia

AU - Han, Sangjo

AU - Jeffery, Linda

AU - Baek, Seung Tae

AU - Lee, Hyemi

AU - Shim, Young Sam

AU - Lee, Minho

AU - Kim, Lila

AU - Heo, Kyung Sun

AU - Noh, Eun Joo

AU - Lee, Ah Reum

AU - Jang, Young Joo

AU - Chung, Kyung Sook

AU - Choi, Shin Jung

AU - Park, Jo Young

AU - Park, Youngwoo

AU - Kim, Hwan Mook

AU - Park, Song Kyu

AU - Park, Hae Joon

AU - Kang, Eun Jung

AU - Kim, Hyong Bai

AU - Kang, Hyun Sam

AU - Park, Hee Moon

AU - Kim, Kyunghoon

AU - Song, Kiwon

AU - Song, Kyung Bin

AU - Nurse, Paul

AU - Hoe, Kwang Lae

N1 - Funding Information: Y.-D. Kim, S. Park, H.-J. Lee, J.-H. Ahn, Y.-S. Kil, S.-Y. Park, J.-H. Lim, J.-H. Song, Y.-K. Ryoo, J.-Y. Kim, M.-J. Oh, S. Kong, J. Ahn, N. Sun, N. Peat, R. Mandeville and J.-J. Li. We also thank J.-H. Roe and W.-K. Huh for reading this manuscript and for their insightful comments and O. Nielsen for his patience with the many requests for pON177. This work was supported by the intramural research program of KRIBB (Mission 2007), the Chemical Genomics Research Program and the 21st Century Frontier Research Program from the Ministry of Education, Science and Technology (MOEST) of Korea. This work was also supported by Bioneer Corp., The Wellcome Trust, Cancer Research UK, The Breast Cancer Research Foundation (BCRF) and The Rockefeller University.

PY - 2010/6

Y1 - 2010/6

N2 - We report the construction and analysis of 4,836 heterozygous diploid deletion mutants covering 98.4% of the fission yeast genome providing a tool for studying eukaryotic biology. Comprehensive gene dispensability comparisons with budding yeastthe only other eukaryote for which a comprehensive knockout library existsrevealed that 83% of single-copy orthologs in the two yeasts had conserved dispensability. Gene dispensability differed for certain pathways between the two yeasts, including mitochondrial translation and cell cycle checkpoint control. We show that fission yeast has more essential genes than budding yeast and that essential genes are more likely than nonessential genes to be present in a single copy, to be broadly conserved and to contain introns. Growth fitness analyses determined sets of haploinsufficient and haploproficient genes for fission yeast, and comparisons with budding yeast identified specific ribosomal proteins and RNA polymerase subunits, which may act more generally to regulate eukaryotic cell growth.

AB - We report the construction and analysis of 4,836 heterozygous diploid deletion mutants covering 98.4% of the fission yeast genome providing a tool for studying eukaryotic biology. Comprehensive gene dispensability comparisons with budding yeastthe only other eukaryote for which a comprehensive knockout library existsrevealed that 83% of single-copy orthologs in the two yeasts had conserved dispensability. Gene dispensability differed for certain pathways between the two yeasts, including mitochondrial translation and cell cycle checkpoint control. We show that fission yeast has more essential genes than budding yeast and that essential genes are more likely than nonessential genes to be present in a single copy, to be broadly conserved and to contain introns. Growth fitness analyses determined sets of haploinsufficient and haploproficient genes for fission yeast, and comparisons with budding yeast identified specific ribosomal proteins and RNA polymerase subunits, which may act more generally to regulate eukaryotic cell growth.

UR - http://www.scopus.com/inward/record.url?scp=77953255163&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77953255163&partnerID=8YFLogxK

U2 - 10.1038/nbt.1628

DO - 10.1038/nbt.1628

M3 - Article

C2 - 20473289

AN - SCOPUS:77953255163

SN - 1087-0156

VL - 28

SP - 617

EP - 623

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 6

ER -

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this