Cited by 604Fungal and yeast genetics researchBioinformatics and Genomic NetworksGenomics and Chromatin Dynamics

Exploration of Essential Gene Functions via Titratable Promoter Alleles

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Mnaimneh, Sanie, Davierwala, Armaity P, Haynes, Jennifer, Moffat, Jason, Peng, Wen-Tao, Zhang, Wen, Yang, Xueqi, Pootoolal, Jeff +16 more·2004·Cell

Abstract

Nearly 20% of yeast genes are required for viability, hindering genetic analysis with knockouts. We created promoter-shutoff strains for over two-thirds of all essential yeast genes and subjected them to morphological analysis, size profiling, drug sensitivity screening, and microarray expression profiling. We then used this compendium of data to ask which phenotypic features characterized different functional classes and used these to infer potential functions for uncharacterized genes. We identified genes involved in ribosome biogenesis (HAS1, URB1, and URB2), protein secretion (SEC39), mitochondrial import (MIM1), and tRNA charging (GSN1). In addition, apparent negative feedback transcriptional regulation of both ribosome biogenesis and the proteasome was observed. We furthermore show that these strains are compatible with automated genetic analysis. This study underscores the importance of analyzing mutant phenotypes and provides a resource to complement the yeast knockout collection.

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Crossref · 10.1016/j.cell.2004.06.013

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  • Essential genes participated in ~5-fold more negative and positive interactions than nonessential genes.

    “In general, essential genes participated in ~5-fold more negative and positive interactions than nonessential genes, confirming previous estimates (Fig. 5A)(24).”
  • Essential genes are major hubs and form the basic scaffold of the global genetic interaction network.

    “First, consistent with the results of our previous smaller scale surveys (1, 24), essential genes are major hubs and form the basic scaffold of the global genetic interaction network.”

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Research works printed but not linked: 3

  1. [45]45. Oba, S. ∙ Sato, M. ∙ Takemasa, I. ... A Bayesian missing value estimation method Bioinformatics. 2003; 19:2088-2096 Crossref Scopus (582) PubMed Google Scholar
  2. [48]48. Robinson, M.D. ∙ Grigull, J. ∙ Mohammad, N. ... FunSpeca web-based cluster interpreter for yeast BMC Bioinformatics. 2002; 3:35 Crossref Scopus (330) PubMed Google Scholar
  3. [50]50. Sachs, L. Applied Statistics.Springer-Verlag, Berlin, 1982 Crossref Google Scholar

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Authors
Mnaimneh, S., Davierwala, A. P., Haynes, J., Moffat, J., Peng, W.-T., Zhang, W., Yang, X., Pootoolal, J., Chua, G., Lopez, A., Trochesset, M., Morse, D., Krogan, N. J., Hiley, S. L., Li, Z., Morris, Q., Grigull, J., Mitsakakis, N., Roberts, C. J., Greenblatt, J. F., Boone, C., Kaiser, C. A., Andrews, B. J., & Hughes, T. R.
Affiliations
  • University of Toronto (CA)
  • Massachusetts Institute of Technology (US)
  • Merck & Co., Inc., Rahway, NJ, USA (United States) (US)
Corresponding author
Hughes, Timothy R
Venue
Cell
Publisher
Elsevier BV
Published
2004-07
Volume
118
Issue
1
Pages
31-44
ISSN
0092-8674 (ISSN-L)
OpenAlex
W1974220691
Cited by
604
References
64
Citations by year
2026: 6 · 2025: 11 · 2024: 17 · 2023: 15 · 2022: 22 · 2021: 21 · 2020: 14 · 2019: 17 · 2018: 17 · 2017: 21 · 2016: 23 · 2015: 26 · 2014: 30 · 2013: 28 · 2012: 32
FWCI
14.21
Type
journal article
Language
en
Open access
Locations
  • Cell (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
essential genes, Saccharomyces cerevisiae, gene function prediction, ribosome biogenesis, protein secretion, mitochondrial protein import, aminoacylation, proteasome, mutant phenotypes
MeSH terms
Alleles, Pharmaceutical Preparations, Genes, Fungal, Mitochondria, Models, Genetic, Promoter Regions, Genetic, Protein Processing, Post-Translational, Ribosomal Proteins, RNA, Transfer, Saccharomyces cerevisiae, Transcription, Genetic, Gene Expression Regulation, Fungal, Gene Deletion, Genes, Essential, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Feedback, Physiological, Saccharomyces cerevisiae Proteins

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