The DOI matches its Crossref record; 64 of the 64 references it cites were found in a registry or an index.
Exploration of Essential Gene Functions via Titratable Promoter Alleles
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“In general, essential genes participated in ~5-fold more negative and positive interactions than nonessential genes, confirming previous estimates (Fig. 5A)(24).”
From A global genetic interaction network maps a wiring diagram of cellular function (2016) · cites this paper as [24]
In the citing paper
“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.”
From A global genetic interaction network maps a wiring diagram of cellular function (2016) · cites this paper as [24]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Neural networks for pattern recognition
Bishop, C. (1994) · Choice Reviews Online · doi:10.5860/choice.31-5500 · Cited by 18,537
Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 16,184
Functional organization of the yeast proteome by systematic analysis of protein complexes
Gavin, A., Böesche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A., Cruciat, C., et al. (2002) · Nature · doi:10.1038/415141a · Cited by 4,729
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706
Functional profiling of the Saccharomyces cerevisiae genome
Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316
Self-citationGlobal analysis of protein localization in budding yeast
Huh, W.-K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., & O'Shea, E. K. (2003) · Nature · doi:10.1038/nature02026 · Cited by 4,248 · cited 1×
“the nucleolus (Huh et al., 2003) ,”
Global analysis of protein expression in yeast
Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., & Weissman, J. S. (2003) · Nature · doi:10.1038/nature02046 · Cited by 3,750
Yang, Y., Dudoit, S., Luu, P., Lin, D., Peng, V., Ngai, J., & Speed, T. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.4.e15 · Cited by 3,722
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Ho, Y., Gruhler, A., Heilbut, A. M., Bader, G. D., Moore, L., Adams, S., Millar, A., Taylor, P. P., Bennett, K. L., Boutilier, K., et al. (2002) · Nature · doi:10.1038/415180a · Cited by 3,573
Flagged first, then by citations
Research works printed but not linked: 3
- Ashburner, 2000, Gene ontology, The Gene Ontology Consortium. Nat. Genet., 25, 25
- Barnes, 1984, Asparagine-linked glycosylation in Saccharomyces cerevisiae, Mol. Cell. Biol., 4, 2381
- Vazquez de Aldana, 1994, Multicopy tRNA genes functionally suppress mutations in yeast eIF-2 alpha kinase GCN2, Mol. Cell. Biol., 14, 7920
Cited by
Sorted by citations
A global genetic interaction network maps a wiring diagram of cellular function
Costanzo, M., VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., et al. (2016) · Science · doi:10.1126/science.aaf1420 · Cited by 1,240
“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.”
ResultSelf-citationSgs1 Helicase and Two Nucleases Dna2 and Exo1 Resect DNA Double-Strand Break Ends
Zhu, Z., Chung, W.-H., Shim, E. Y., Lee, S. E., & Ira, G. (2008) · Cell · doi:10.1016/j.cell.2008.08.037 · Cited by 1,108
“Instead we constructed DNA2 under the regulatable TetO 7 promoter in which DNA2 expression is shut off by the addition of doxocycline to the growth media (Mnaimneh et al., 2004).”
Tuning genetic control through promoter engineering
Alper, H. S., Fischer, C. R., Nevoigt, E., & Stephanopoulos, G. N. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504604102 · Cited by 894
Schuldiner, M., Collins, S. R., Thompson, N. J., Denic, V., Bhamidipati, A., Punna, T., Ihmels, J., Andrews, B., Boone, C., Greenblatt, J. F., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.031 · Cited by 870
“DAmP utilizes simple, PCR-based homologous recombination to disrupt the natural 3#UTR by insertion of an antibiotic-resistance marker, thus greatly destabilizing the corresponding messages (Muhlrad and Parker, 1999).”
MethodSelf-citationGene essentiality and synthetic lethality in haploid human cells
Blomen, V. A., Májek, P., Jae, L. T., Bigenzahn, J. W., Nieuwenhuis, J., Staring, J., Sacco, R., van Diemen, F. R., Olk, N., Stukalov, A., et al. (2015) · Science · doi:10.1126/science.aac7557 · Cited by 857
Mitochondrial protein import: from proteomics to functional mechanisms
Schmidt, O., Pfanner, N., & Meisinger, C. (2010) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2959 · Cited by 717
Mapping Pathways and Phenotypes by Systematic Gene Overexpression
Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K. A., Snyder, M., Oliver, S. G., Cyert, M., Hughes, T. R., et al. (2006) · Molecular Cell · doi:10.1016/j.molcel.2005.12.011 · Cited by 665
“The genetic accessibility of the budding yeast S. cerevisiae has allowed the development of genome-wide loss-of-function mutant collections , including gene deletion (Giaever et al., 2002) and titratable promoter alleles (Mnaimneh et al., 2004), for systematic scrutiny of gene function.”
BackgroundMethodSelf-citationExploring genetic interactions and networks with yeast
Boone, C., Bussey, H., & Andrews, B. J. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2085 · Cited by 661
Efflux-Mediated Antifungal Drug Resistance
Cannon, R. D., Lamping, E., Holmes, A. R., Niimi, K., Baret, P. V., Keniya, M. V., Tanabe, K., Niimi, M., Goffeau, A., & Monk, B. C. (2009) · Clinical Microbiology Reviews · doi:10.1128/cmr.00051-08 · Cited by 608
“In addition to a panel of haploid mutants in which each nonessential gene has been knocked out (385), there is a panel of haploid strains in which the activities of many essential genes can be titrated using the Tet promoter (141, 225), and there is a panel of heterozygous diploid mutants in which individual essential…”
BackgroundProgress in Metabolic Engineering of Saccharomyces cerevisiae
Nevoigt, E. (2008) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00025-07 · Cited by 597
“Recently the bacterial tet promoter system has been used for inducer-triggered repression of all essential genes in yeast (225, 402).”
MethodMechanisms of Haploinsufficiency Revealed by Genome-Wide Profiling in Yeast
Deutschbauer, A. M., Jaramillo, D. F., Proctor, M., Kumm, J., Hillenmeyer, M. E., Davis, R. W., Nislow, C., & Giaever, G. (2005) · Genetics · doi:10.1534/genetics.104.036871 · Cited by 535
“2003; Mnaimneh et al. 2004).”
A comprehensive strategy enabling high-resolution functional analysis of the yeast genome
Breslow, D. K., Cameron, D. M., Collins, S. R., Schuldiner, M., Stewart-Ornstein, J., Newman, H. W., Braun, S. J., Madhani, H. D., Krogan, N. J., & Weissman, J. S. (2008) · Nature Methods · doi:10.1038/nmeth.1234 · Cited by 536
“Essential genes are a highly conserved and medically relevant gene subset, with ∼40% having counterparts in human”
BackgroundSelf-citationThe GET Complex Mediates Insertion of Tail-Anchored Proteins into the ER Membrane
Schuldiner, M., Metz, J., Schmid, V., Denic, V., Rakwalska, M., Schmitt, H. D., Schwappach, B., & Weissman, J. S. (2008) · Cell · doi:10.1016/j.cell.2008.06.025 · Cited by 522
“The tetO7-SED5 strain was picked from the essential gene promoter shut-off collection (Mnaimneh et al., 2004).”
BackgroundSynthetic Genetic Array Analysis in Saccharomyces cerevisiae
Tong, A. H. Y., & Boone, C. M. (2005) · Humana Press eBooks · doi:10.1385/1-59259-958-3:171 · Cited by 489
Self-citationThe dependence of viral RNA replication on co-opted host factors
Nagy, P. D., & Pogany, J. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2692 · Cited by 447
Jerónimo, C., Forget, D., Bouchard, A., Li, Q., Chua, G., Poitras, C., Thérien, C., Bergeron, D., Bourassa, S., Greenblatt, J., et al. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.06.027 · Cited by 444
“(D) Clustering analysis of mRNA expression profiles with tet-promoter alleles corresponding to RBA50, NPA3, YLR243W, and RPB11, in comparison to profiles from 214 other tet-promoter mutants representing diverse cellular functions (Mnaimneh et al., 2004).”
MethodResultInfluentialSelf-citationSystematic humanization of yeast genes reveals conserved functions and genetic modularity
Kachroo, A. H., Laurent, J. M., Yellman, C. M., Meyer, A. G., Wilke, C. O., & Marcotte, E. M. (2015) · Science · doi:10.1126/science.aaa0769 · Cited by 447
Genetic reconstruction of a functional transcriptional regulatory network
Hu, Z., Killion, P. J., & Iyer, V. R. (2007) · Nature Genetics · doi:10.1038/ng2012 · Cited by 416
“For the essential transcription factor HSF1 , we used a conditional shut-off strain 12 .”
MethodSystematic exploration of essential yeast gene function with temperature-sensitive mutants
Li, Z., Vizeacoumar, F. J., Bahr, S., Li, J., Warringer, J., Vizeacoumar, F. S., Min, R., VanderSluis, B., Bellay, J., DeVit, M. J., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1832 · Cited by 428
Self-citationControlling gene expression in mycobacteria with anhydrotetracycline and Tet repressor
Ehrt, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gni013 · Cited by 383
“Inducible gene expression systems are powerful tools for studying gene function and for the validation of drug targets in bacteria (4,5).”
BackgroundPark, S.-H., Kukushkin, Y., Gupta, R., Chen, T., Konagai, A., Hipp, M. S., Hayer-Hartl, M. K., & Hartl, F. U. (2013) · Cell · doi:10.1016/j.cell.2013.06.003 · Cited by 368
A Role for Phosphatidic Acid in the Formation of “Supersized” Lipid Droplets
Fei, W., Shui, G., Zhang, Y., Krahmer, N., Ferguson, C., Kapterian, T. S., Lin, R. C. Y., Dawes, I. W., Brown, A. J., Li, P., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002201 · Cited by 358
“In order to identify essential genes impacting LD size, we now included the collection of mutants where all essential genes are controlled by the TetO7-promoter, which can be switched off efficiently [24].”
BackgroundTrait Variation in Yeast Is Defined by Population History
Warringer, J., Zörgö, E., Cubillos, F. A., Zia, A., Gjuvsland, A. B., Simpson, J. T., Forsmark, A., Durbin, R. M., Omholt, S. W., Louis, E. J., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002111 · Cited by 338
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks
di Bernardo, D., Thompson, M. J., Gardner, T. S., Chobot, S. E., Eastwood, E. L., Wojtovich, A. P., Elliott, S. J., Schaus, S. E., & Collins, J. J. (2005) · Nature Biotechnology · doi:10.1038/nbt1075 · Cited by 349
25 Yeast Genetic Strain and Plasmid Collections
Entian, K., & Kötter, P. (2007) · Methods in microbiology · doi:10.1016/s0580-9517(06)36025-4 · Cited by 310
Systematic Mapping of Genetic Interaction Networks
Dixon, S. J., Costanzo, M., Baryshnikova, A., Andrews, B., & Boone, C. M. (2008) · Annual Review of Genetics · doi:10.1146/annurev.genet.39.073003.114751 · Cited by 298
“An extensive set of promoter shut-off strains, in which each essential gene is placed under the control of a repressible promoter (TET-alleles), has been constructed and combined with SGA to produce a genetic interaction network comprising 567 essential gene interactions (27, 88).”
Self-citationEmerging and evolving concepts in gene essentiality
Rancati, G. I., Moffat, J., Typas, A., & Pavelka, N. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.74 · Cited by 279
Self-citationTunable and reversible drug control of protein production via a self-excising degron
Chung, H. K., Jacobs, C. L., Huo, Y., Yang, J., Krumm, S. A., Plemper, R. K., Tsien, R. Y., & Lin, M. Z. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1869 · Cited by 233
The synthetic genetic interaction spectrum of essential genes
Davierwala, A. P., Haynes, J., Li, Z., Brost, R. L., Robinson, M. D., Yu, L. X., Mnaimneh, S., Ding, H., Zhu, H., Chen, Y., et al. (2005) · Nature Genetics · doi:10.1038/ng1640 · Cited by 221
Self-citationBen‐Aroya, S., Coombes, C. E., Kwok, T., O’Donnell, K. A., Boeke, J. D., & Hieter, P. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.02.021 · Cited by 213
“This approach has recently been used to generate a collection of promoter-shutoff strains for two-thirds of the essential yeast gene (Mnaimneh et al., 2004).”
BackgroundMethodSynthetic Genetic Array (SGA) Analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe
Baryshnikova, A., Costanzo, M., Dixon, S. J., Vizeacoumar, F. J., Myers, C. L., Andrews, B., & Boone, C. M. (2010) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(10)70007-0 · Cited by 212
Self-citationOne library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy
Yofe, I., Weill, U., Meurer, M., Chuartzman, S. G., Zalckvar, E., Goldman, O., Ben‐Dor, S., Schütze, C., Wiedemann, N., Knop, M., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3795 · Cited by 211
Reversible protein aggregation is a protective mechanism to ensure cell cycle restart after stress
Saad, S., Cereghetti, G., Feng, Y., Picotti, P., Peter, M., & Dechant, R. C. (2017) · Nature Cell Biology · doi:10.1038/ncb3600 · Cited by 186
RSC Mobilizes Nucleosomes To Improve Accessibility of Repair Machinery to the Damaged Chromatin
Shim, E. Y., Hong, S. J., Oum, J.-H., Yanez, Y., Zhang, Y., & Lee, S. E. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.01956-06 · Cited by 183
“Instead of using these rsc mutants, we established a donorless yeast strain with the key ATPase subunit (Sth1) of the RSC complex under the control of the Tet-off system and the galactose-inducible HO integrated at the ade3 locus (29).”
MethodZhao, R., Kakihara, Y., Gribun, A., Huen, J., Yang, G., Khanna, M., Costanzo, M., Brost, R. L., Boone, C. M., Hughes, T. R., et al. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200709061 · Cited by 185
Self-citationIdentifying transcription factor functions and targets by phenotypic activation
Chua, G., Morris, Q., Sopko, R., Robinson, M. D., Ryan, O. W., Chan, E. T., Frey, B. J., Andrews, B., Boone, C. M., & Hughes, T. R. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605140103 · Cited by 183
Self-citationFang, N. N., Chan, G. T., Zhu, M., Comyn, S. A., Persaud, A. K., Deshaies, R. J., Rotin, D., Gsponer, J., & Mayor, T. (2014) · Nature Cell Biology · doi:10.1038/ncb3054 · Cited by 179
Cryo-EM structure of the mitochondrial protein-import channel TOM complex at near-atomic resolution
Tucker, K., & Park, E. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0339-2 · Cited by 161
Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics
Li, Z., Lee, I., Moradi, E. K., Hung, N., Johnson, A. M., & Marcotte, E. M. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000213 · Cited by 180
“TetO7-promoter mutants [28] and TAPtagged strains [31] were acquired from Open Biosystems.”
MethodSelf-citationEssence of life: essential genes of minimal genomes
Juhas, M., Eberl, L., & Glass, J. I. (2011) · Trends in Cell Biology · doi:10.1016/j.tcb.2011.07.005 · Cited by 178
Assembly of the PtdIns 4-kinase Stt4 complex at the plasma membrane requires Ypp1 and Efr3
Baird, D., Stefan, C. J., Audhya, A., Weys, S., & Emr, S. D. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200804003 · Cited by 172
“We conclude that Ypp1 and Stt4 rely on each other to maintain their localization such that recruitment and stability of the PIK patch at the PM depends on an intact Stt4 – Ypp1 complex.”
InfluentialStirling, P. C., Bloom, M. S., Solanki-Patil, T., Smith, S. N., Sipahimalani, P., Li, Z., Kofoed, M., Ben‐Aroya, S., Myung, K., & Hieter, P. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002057 · Cited by 166
Self-citationWang, R., & Nagy, P. D. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.02.005 · Cited by 167
“In this system, the expression of TDH3 can be downregulated by addition of various amounts of doxycycline to the yeast growth medium, as is widely used for the construction of the yeast essential gene library (yTHC) (Mnaimneh et al., 2004).”
MethodYeast as a Model Host to Explore Plant Virus-Host Interactions
Nagy, P. D. (2008) · Annual Review of Phytopathology · doi:10.1146/annurev.phyto.121407.093958 · Cited by 166
“The downregulatable essential-gene library (yTHC) covering ∼15% of yeast genes has also been created (66).”
Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L
Huber, A., French, S. L., Tekotte, H., Yerlikaya, S., Ståhl, M., Perepelkina, M. P., Tyers, M., Rougemont, J., Beyer, A. L., & Loewith, R. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.221 · Cited by 166
“This negative transcriptional feedback mechanism in principle imposes homeostatic control on Ribi (Supplementary Figure S6), and may act in concert with previously reported signalling feedback loops on Sch9 and Sfp1 (Jorgensen et al, 2004; Mnaimneh et al, 2004; Lempiainen et al, 2009).”
Role of Essential Genes in Mitochondrial Morphogenesis inSaccharomyces cerevisiae
Altmann, K., & Westermann, B. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e05-07-0678 · Cited by 165
Tam41 Is a CDP-Diacylglycerol Synthase Required for Cardiolipin Biosynthesis in Mitochondria
Tamura, Y., Harada, Y., Nishikawa, S., Yamano, K., Kamiya, M., Shiota, T., Kuroda, T., Kuge, O., Sesaki, H., Imai, K., et al. (2013) · Cell Metabolism · doi:10.1016/j.cmet.2013.03.018 · Cited by 163
“To test this possibility, we utilized the yeast strain expressing Cds1FLAG under the control of the TetO7 promoter (Mnaimneh et al., 2004) and examined CDP-DAG synthase activities of mitochondria purified from the cells with or without Cds1FLAG depletion by addition of doxycycline.”
Fendt, S., Buescher, J. M., Rudroff, F., Picotti, P., Zamboni, N., & Sauer, U. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.11 · Cited by 159
“Tet-titratable promotor strains were obtained from openbiosystem (Mnaimneh et al, 2004).”
MethodSystems-level antimicrobial drug and drug synergy discovery
Roemer, T., & Boone, C. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1205 · Cited by 159
Self-citationCreamer, T. J., Darby, M. M., Jamonnak, N., Schaughency, P., Hao, H., Wheelan, S. J., & Corden, J. L. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002329 · Cited by 173
“RNA derived from wild-type cells or cells in which Nrd1 expression is regulated by a Tet promoter”
BackgroundBiogenesis of the Mitochondrial TOM Complex
Becker, T., Pfannschmidt, S., Guiard, B., Stojanovski, D., Milenkovic, D., Kutik, S., Pfanner, N., Meisinger, C., & Wiedemann, N. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m706997200 · Cited by 153
Boczonadi, V., Müller, J. S., Pyle, A., Munkley, J., Dor, T., Quartararo, J., Ferrero, I., Karcagi, V., Giunta, M., Polvikoski, T., et al. (2014) · Nature Communications · doi:10.1038/ncomms5287 · Cited by 149
Regulation of Yeast NRD1 Expression by Premature Transcription Termination
Arigo, J. T., Carroll, K. L., Ames, J. M., & Corden, J. L. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.02.005 · Cited by 144
GeneWeaver: a web-based system for integrative functional genomics
Baker, E. J., Jay, J. J., Bubier, J. A., Langston, M. A., & Chesler, E. J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr968 · Cited by 140
Ergosterol content specifies targeting of tail-anchored proteins to mitochondrial outer membranes
Krumpe, K., Frumkin, I., Herzig, Y., Rimon, N., Özbalci, C., Brügger, B., Rapaport, D., & Schuldiner, M. (2012) · Molecular Biology of the Cell · doi:10.1091/mbc.e11-12-0994 · Cited by 143
“For example, in yeast, TA proteins are required for mitochondrial fission (Fis1; Mozdy et al. , 2000), for inheritance and motility (Gem1; Frederick et al. , 2004) and for the functioning of the translocase of the outer membrane (TOM) complex (Tom5, Tom6, and Tom7; Walther and Rapaport, 2009).”
BackgroundMethodBiogenesis of β-barrel membrane proteins of mitochondria
Paschen, S. A., Neupert, W., & Rapaport, D. (2005) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.08.009 · Cited by 137
Dechant, R. C., Saad, S., Ibáñez, A. J., & Peter, M. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.06.002 · Cited by 138
“Therefore, we studied the influence of Pma1 activity on cell growth using a doxycycline-repressible allele (tetO7-PMA1; Mnaimneh et al., 2004).”
A prototrophic deletion mutant collection for yeast metabolomics and systems biology
Mülleder, M., Capuano, F., Pir, P., Christen, S., Sauer, U., Oliver, S. G., & Ralser, M. (2012) · Nature Biotechnology · doi:10.1038/nbt.2442 · Cited by 133
Li, Z., Barajas, D., Panavas, T., Herbst, D. A., & Nagy, P. D. (2008) · Journal of Virology · doi:10.1128/jvi.00702-08 · Cited by 132
“To test if downregulation of the Cdc34p level affects TBSV repRNA accumulation, we used doxycycline-regulatable expression of Cdc34p from its original chromosomal location ( 25 ).”
MethodSelf-citationNedea, E. C., Nalbant, D., Xia, D., Theoharis, N. T., Suter, B., Richardson, C. J., Tatchell, K., Kislinger, T., Greenblatt, J. F., & Nagy, P. L. (2008) · Molecular Cell · doi:10.1016/j.molcel.2007.12.031 · Cited by 128
“The growth rate of the ref2D sen1tetO7 double mutant (Mnaimneh et al., 2004) was estimated by serial dilution of strains on YPD medium in the presence or absence of 10 mg/ml doxycycline.”
MethodSelf-citationCharging it up: global analysis of protein phosphorylation
Ptacek, J., & Snyder, M. P. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.08.005 · Cited by 128
Aoki, T., Ichimura, S., Itoh, A., Kuramoto, M., Shinkawa, T., Isobe, T., & Tagaya, M. (2009) · Molecular Biology of the Cell · doi:10.1091/mbc.e08-11-1104 · Cited by 125
“27 (Mnaimneh et al., 2004; Kraynack et al., 2005).”
van Bakel, H., Tsui, K., Gebbia, M., Mnaimneh, S., Hughes, T. R., & Nislow, C. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003479 · Cited by 124
“These conditions were previously shown to lead to effective ablation of proteins encoded by essential genes [74].”
BackgroundMethodSelf-citationIn Vivo Robustness Analysis of Cell Division Cycle Genes in Saccharomyces cerevisiae
Moriya, H., Shimizu‐Yoshida, Y., & Kitano, H. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020111 · Cited by 125
“For example, in model organisms such as Saccharomyces cerevisiae, comprehensive gene knockout or promoter titration analyses have been performed [9,10].”
BackgroundDown-Regulating Sphingolipid Synthesis Increases Yeast Lifespan
Huang, X., Liu, J., & Dickson, R. C. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002493 · Cited by 127
Altmann, K., Frank, M., Neumann, D., Jakobs, S., & Westermann, B. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200709099 · Cited by 130
Jiang, Y., Servienė, E., Gál, J., Panavas, T., & Nagy, P. D. (2006) · Journal of Virology · doi:10.1128/jvi.02686-05 · Cited by 122
“For maximum level of essential gene expression, yeast was grown in the absence of doxycycline, whereas to reduce the expression levels of the essential genes, yeast was grown in the same medium in the presence of 10 mg/liter doxycycline ( 17 ).”
BackgroundMethodInfluentialGlobal Map of SUMO Function Revealed by Protein-Protein Interaction and Genetic Networks
Makhnevych, T., Sydorskyy, Y., Xin, X., Srikumar, T., Vizeacoumar, F. J., Jeram, S. M., Li, Z., Bahr, S., Andrews, B., Boone, C. M., et al. (2009) · Molecular Cell · doi:10.1016/j.molcel.2008.12.025 · Cited by 125
Self-citation16 High-Throughput Strain Construction and Systematic Synthetic Lethal Screening in
Tong, A. H. Y., & Boone, C. M. (2007) · Methods in microbiology · doi:10.1016/s0580-9517(06)36016-3 · Cited by 121
Self-citationA general lack of compensation for gene dosage in yeast
Springer, M., Weissman, J. S., & Kirschner, M. W. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.19 · Cited by 123
“Compensators are rare among essential genes and overexpressed genes To test whether essential (Ess) genes behave differently from non-essential genes, we created 40 diploid strains where one copy of an essential gene was fused to GFP and the second copy was under the control of doxycycline (EssX-GFP/TetO 7pr -EssX)”
BackgroundMultiple pathways in the integration of proteins into the mitochondrial outer membrane
Dukanovic, J., & Rapaport, D. (2010) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2010.06.021 · Cited by 123
Escobar‐Henriques, M., Westermann, B., & Langer, T. (2006) · The Journal of Cell Biology · doi:10.1083/jcb.200512079 · Cited by 119
“We also analyzed the stability of Fzo1 in cells that allow tetracycline-sensitive expression of the essential genes CDC53 and CDC34 (Mnaimneh et al., 2004) but did not observe a stabilization of Fzo1 upon repression of CDC53 or CDC34 (unpublished data).”
BackgroundAdvanced Methods for High-Throughput Microscopy Screening of Genetically Modified Yeast Libraries
Cohen, Y., & Schuldiner, M. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-276-2_8 · Cited by 117
“To study the proteins that are required for such cellular processes, these markers should be studied on the background of systematic libraries of mutants, such as the deletion library for nonessential proteins (27), several different libraries allowing downregulation or destabilization of essential proteins (such as t…”
BackgroundStill Stratus Not Altocumulus: Further Evidence against the Date/Party Hub Distinction
Batada, N. N., Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B., Hurst, L. D., & Tyers, M. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050154 · Cited by 113
Cellular and mitochondrial remodeling upon defects in iron-sulfur protein biogenesis
Hausmann, A., Samans, B., Lill, R., & Mühlenhoff, U. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m705570200 · Cited by 111
Popov-Celeketic, J., Waizenegger, T., & Rapaport, D. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.12.006 · Cited by 111
Boutros, P. C., & Okey, A. B. (2005) · Briefings in Bioinformatics · doi:10.1093/bib/6.4.331 · Cited by 109
“In yeast, this work has been extended to include both knockouts of non-essential genes and knockdowns of essential genes, allowing the effects of genetic perturbation of every single gene to be exploited for identification of co-regulation.(51) This type of integration of expression data with functional annotation has…”
BackgroundGenetic Interaction Networks: Toward an Understanding of Heritability
Baryshnikova, A., Costanzo, M., Myers, C. L., Andrews, B., & Boone, C. M. (2013) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082509-141730 · Cited by 112
Self-citationNucleolar URB1 ensures 3′ ETS rRNA removal to prevent exosome surveillance
Shan, L., Xu, G., Yao, R.-W., Luan, P.-F., Huang, Y., Zhang, P.-H., Pan, Y.-H., Zhang, L., Gao, X., Li, Y., et al. (2023) · Nature · doi:10.1038/s41586-023-05767-5 · Cited by 111
“Depletion of the URB1 and URB2 homologues Npa1p and Npa2p, respectively, in yeast is lethal, and Npa1p appears to be essential for pre-rRNA processing and ribosome biogenesis, but the precise roles of Npa1p and Npa2p are unclear 20,21 .”
Hulett, J. M., Lueder, F., Chan, N. C., Perry, A., Wolynec, P. P., Likić, V. A., Gooley, P. R., & Lithgow, T. J. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.12.021 · Cited by 109
Biosynthesis of isoprenoids, polyunsaturated fatty acids and flavonoids in Saccharomyces cerevisiae
Chemler, J. A., Yan, Y., & Koffas, M. A. G. (2006) · Microbial Cell Factories · doi:10.1186/1475-2859-5-20 · Cited by 113
Essential genes as antimicrobial targets and cornerstones of synthetic biology
Juhas, M., Eberl, L., & Church, G. M. (2012) · Trends in biotechnology · doi:10.1016/j.tibtech.2012.08.002 · Cited by 110
Raskin, D. M., Judson, N., & Mekalanos, J. J. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611650104 · Cited by 108
Analysis of Transcriptional Activation at a Distance in Saccharomyces cerevisiae
Dobi, K. C., & Winston, F. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.00459-07 · Cited by 110
“For the systematic genetic array analysis, we screened both the yeast nonessential deletion set (73) and a doxycycline-repressible set of essential genes ( 53 ) by crossing each set to strain FY2584 and screening for growth on SC-His Gal.”
BackgroundMethodInfluentialKraynack, B. A., Chan, A., Rosenthal, E. H., Essid, M., Umansky, B., Waters, M. G., & Schmitt, H. D. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e05-01-0056 · Cited by 106
Efficient protein depletion by genetically controlled deprotection of a dormant N‐degron
Taxis, C., Stier, G., Spadaccini, R., & Knop, M. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.25 · Cited by 107
“…protein destabilization, and heat or small molecule-regulated N-degrons for induced protein degradation (Dohmen et al, 1994; Stack et al, 2000; Mnaimneh et al, 2004; Dohmen and Varshavsky, 2005; Banaszynski et al, 2006; Suter et al, 2006; Boutros and Ahringer, 2008) are highly useful tools to…”
BackgroundМаксимова, Н. Р., Hara, K., Nikolaeva, I., Chun-Feng, T., Usui, T., Takagi, M., Nishihira, Y., Miyashita, A., Fujiwara, H., Oyama, T., et al. (2010) · Journal of Medical Genetics · doi:10.1136/jmg.2009.074815 · Cited by 106
“Although the function of NBAS remains unknown, it has two putative leucine zippers, a ribosomal S14 motif and a domain homologous to secretary pathway protein in yeast, Sec39.”
BackgroundYan, Z., Costanzo, M., Heisler, L. E., Paw, J., Kaper, F., Andrews, B., Boone, C. M., Giaever, G. N., & Nislow, C. (2008) · Nature Methods · doi:10.1038/nmeth.1231 · Cited by 105
Self-citationCharacterization of a Dual Rac/Cdc42 Inhibitor MBQ-167 in Metastatic Cancer
Humphries‐Bickley, T., Castillo‐Pichardo, L., O'Farril, E. H., Borrero-García, L. D., Forestier-Román, I., Gerena, Y., Blanco, M., Rivera-Robles, M. J., Rodríguez-Medina, J. R., Cubano, L. A., et al. (2017) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-16-0442 · Cited by 105
“Using a haploid derivative of the yeast strain BY4741, where the essential gene Cdc42 was knocked out conditionally via a tetracyclineinducible promoter (40), we show thatMBQ-167 exerts a similar phenotype to the cells with reduced Cdc42 expression.”
BackgroundLAS1L interacts with the mammalian Rix1 complex to regulate ribosome biogenesis
Castle, C. D., Cassimere, E. K., & Denicourt, C. (2011) · Molecular Biology of the Cell · doi:10.1091/mbc.e11-06-0530 · Cited by 109
“Real-time PCR analysis was performed on a Light Cycler 480 real-time PCR instrument (Mnaimneh et al. , 2004).”
MethodFadda, A. A., Ryten, M., Droll, D., Rojas, F., Färber, V., Haanstra, J. R., Merce, C., Bakker, B. M., Matthews, K. R., & CLAYTON, C. E. (2014) · Molecular Microbiology · doi:10.1111/mmi.12764 · Cited by 104
“Independently of the method used, transcriptome-wide decay studies can provide insight into the specificity (Grigull et al., 2004; Mnaimneh et al., 2004; Houalla et al., 2006; Chekanova et al., 2007; Kiss and Andrulis, 2010) and dynamics (Gudipati et al.”
MethodHigh-resolution network biology: connecting sequence with function
Ryan, C. J., Cimermančič, P., Szpiech, Z. A., Šali, A., Hernandez, R. D., & Krogan, N. J. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3574 · Cited by 98
Self-citationA Survey of Essential Gene Function in the Yeast Cell Division Cycle
Yu, L. X., Peña‐Castillo, L., Mnaimneh, S., Hughes, T. R., & Brown, G. W. (2006) · Molecular Biology of the Cell · doi:10.1091/mbc.e06-04-0368 · Cited by 102
Self-citationA fast and efficient translational control system for conditional expression of yeast genes
Kötter, P., Weigand, J. E., Meyer, B., Entian, K., & Suess, B. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp578 · Cited by 101
“For two of them, NOP8 and SEC1, attempts to establish conditional regulation using other systems had failed so far (8,28).”
BackgroundConfirmation of Organized Modularity in the Yeast Interactome
Bertin, N., Simonis, N., Dupuy, D., Cusick, M. E., Han, J. J., Fraser, H. B., Roth, F. P., & Vidal, M. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050153 · Cited by 100
Servienė, E., Jiang, Y., Cheng, C., Baker, J., & Nagy, P. D. (2006) · Journal of Virology · doi:10.1128/jvi.80.3.1231-1241.2006 · Cited by 99
Mutations in the Saccharomyces cerevisiae RPB1 Gene Conferring Hypersensitivity to 6-Azauracil
Malagón, F., Kireeva, M. L., Shafer, B. K., Lubkowska, L., Kashlev, M., & Strathern, J. N. (2006) · Genetics · doi:10.1534/genetics.105.052415 · Cited by 99
“…of RNAPII (encoded by RPB1) is essential and we wanted to be able to identify recessive mutations, we developed a screen for rpb1 mutants on the basis of a strain (GRY3019) that contains an RPB1 allele (PtetRPB1) that can be turned off by addition of doxycycline to the media (Mnaimneh et al. 2004).”
BackgroundMethodSimple is good: yeast models of neurodegeneration
Tenreiro, S., & Outeiro, T. F. (2010) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2010.00649.x · Cited by 102
Structural characterization of Tip20p and Dsl1p, subunits of the Dsl1p vesicle tethering complex
Tripathi, A., Ren, Y., Jeffrey, P. D., & Hughson, F. M. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1548 · Cited by 98
Kopajtich, R., Murayama, K., Janecke, A., Haack, T. B., Breuer, M., Knisely, A. S., Harting, I., Ohashi, T., Okazaki, Y., WATANABE, D., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.05.027 · Cited by 97
Metadata
- 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
- ORCID
- 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
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 3303 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
