Exploration of essential gene functions via titratable promoter alleles
Sanie Mnaimneh,Armaity P. Davierwala,Jennifer Haynes,Jason Moffat,Wen-Tao Peng,Wen Zhang,Xueqi Yang,Jeff Pootoolal,Gordon Chua,Andres Lopez,Miles Trochesset,Darcy L Morse,Nevan J. Krogan,Shawna L. Hiley,Zhijian Li,Quaid Morris,Jörg Grigull,Nicholas Mitsakakis,Christopher J. Roberts,Jack Greenblatt,Charles Boone,Chris A. Kaiser,Brenda J. Andrews,Timothy P. Hughes +23 more
TLDR
This study 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, which identified genes involved in ribosome biogenesis, protein secretion, mitochondrial import, and tRNA charging.About:
This article is published in Cell.The article was published on 2004-07-09 and is currently open access. It has received 623 citations till now. The article focuses on the topics: Essential gene & Synthetic genetic array.read more
Citations
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A global genetic interaction network maps a wiring diagram of cellular function
Michael Costanzo,Benjamin VanderSluis,Elizabeth N. Koch,Anastasia Baryshnikova,Carles Pons,Guihong Tan,Wen Wang,Matej Usaj,Julia Hanchard,Susan D. Lee,Vicent Pelechano,Erin B. Styles,Maximilian Billmann,Jolanda van Leeuwen,Nydia Van Dyk,Zhen Yuan Lin,Elena Kuzmin,Justin Nelson,Jeff S. Piotrowski,Tharan Srikumar,Sondra Bahr,Yiqun Chen,Raamesh Deshpande,Christoph F. Kurat,Sheena C. Li,Zhijian Li,Mojca Mattiazzi Usaj,Hiroki Okada,Natasha Pascoe,Bryan Joseph San Luis,Sara Sharifpoor,Emira Shuteriqi,Scott W. Simpkins,Jamie Snider,Harsha Garadi Suresh,Yizhao Tan,Hongwei Zhu,Noël Malod-Dognin,Vuk Janjić,Natasa Przulj,Natasa Przulj,Olga G. Troyanskaya,Igor Stagljar,Tian Xia,Tian Xia,Yoshikazu Ohya,Anne-Claude Gingras,Brian Raught,Michael Boutros,Lars M. Steinmetz,Lars M. Steinmetz,Claire Moore,Adam P. Rosebrock,Amy A. Caudy,Chad L. Myers,Brenda J. Andrews,Charles Boone +56 more
TL;DR: A global genetic interaction network highlights the functional organization of a cell and provides a resource for predicting gene and pathway function and how coherent sets of negative or positive genetic interactions connect protein complex and pathways to map a functional wiring diagram of the cell.
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Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends.
TL;DR: Monitoring 5'-strand resection at inducible DSB ends in yeast and identified proteins required for two stages of resection shows that the Mre11-Rad50-Xrs2 complex (MRX) initiates 5' degradation, whereas Sgs1 and Dna2 degrade 5' strands exposing long 3' strands.
Journal ArticleDOI
Tuning genetic control through promoter engineering
TL;DR: The characterized library of promoters is used to assess the impact of phosphoenolpyruvate carboxylase levels on growth yield and deoxy-xylulose-P synthase Levels on lycopene production and is illustrated as being generalizable to eukaryotic organisms and thus constitutes an integral platform for functional genomics, synthetic biology, and metabolic engineering endeavors.
Journal ArticleDOI
Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray Profile
Maya Schuldiner,Sean R. Collins,Natalie J. Thompson,Vladimir Denic,Arunashree Bhamidipati,Thanuja Punna,Jan Ihmels,Brenda J. Andrews,Charles Boone,Jack Greenblatt,Jonathan S. Weissman,Nevan J. Krogan +11 more
TL;DR: Analysis of an E-MAP of genes acting in the yeast early secretory pathway revealed or clarified the role of many proteins involved in extensively studied processes such as sphingolipid metabolism and retention of HDEL proteins.
Journal ArticleDOI
Gene essentiality and synthetic lethality in haploid human cells
Vincent A. Blomen,Peter Májek,Lucas T. Jae,Johannes W. Bigenzahn,Joppe Nieuwenhuis,Jacqueline Staring,Roberto Sacco,Ferdy R. van Diemen,Nadine Olk,Alexey Stukalov,Caleb D. Marceau,Hans Janssen,Jan E. Carette,Keiryn L. Bennett,Jacques Colinge,Jacques Colinge,Giulio Superti-Furga,Giulio Superti-Furga,Thijn R. Brummelkamp,Thijn R. Brummelkamp +19 more
TL;DR: A synthetic lethality network focused on the secretory pathway based exclusively on mutations was created and revealed a genetic cross-talk governing Golgi homeostasis, an additional subunit of the human oligosaccharyltransferase complex, and a phosphatidylinositol 4-kinase β adaptor hijacked by viruses.
References
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Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
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Neural networks for pattern recognition
TL;DR: This is the first comprehensive treatment of feed-forward neural networks from the perspective of statistical pattern recognition, and is designed as a text, with over 100 exercises, to benefit anyone involved in the fields of neural computation and pattern recognition.
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Cluster analysis and display of genome-wide expression patterns
TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
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Functional organization of the yeast proteome by systematic analysis of protein complexes
Anne-Claude Gavin,Markus Bösche,Roland Krause,Paola Grandi,Martina Marzioch,Andreas Bauer,Jörg Schultz,Jens Rick,Anne-Marie Michon,Cristina-Maria Cruciat,Marita Remor,Christian Höfert,Malgorzata Schelder,Miro Brajenovic,Heinz Ruffner,Alejandro Merino,Karin Klein,Manuela Hudak,David Dickson,Tatjana Rudi,Volker Gnau,Angela Bauch,Sonja Bastuck,Bettina Huhse,Christina Leutwein,Marie-Anne Heurtier,Richard R. Copley,Angela Edelmann,Erich Querfurth,Vladimir Rybin,Gerard Drewes,Manfred Raida,Tewis Bouwmeester,Peer Bork,Bertrand Séraphin,Bernhard Kuster,Gitte Neubauer,Giulio Superti-Furga +37 more
TL;DR: The analysis provides an outline of the eukaryotic proteome as a network of protein complexes at a level of organization beyond binary interactions, which contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery.
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A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Peter Uetz,Loic Giot,Gerard Cagney,Traci A. Mansfield,Richard S. Judson,James R. Knight,Daniel Lockshon,Vaibhav A. Narayan,Maithreyan Srinivasan,Pascale Pochart,Alia Qureshi-Emili,Ying Li,Brian C. Godwin,Diana Conover,Theodore S. Kalbfleisch,Govindan Vijayadamodar,Meijia Yang,Mark Johnston,Stanley Fields,Jonathan M. Rothberg +19 more
TL;DR: Examination of large-scale yeast two-hybrid screens reveals interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes.
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