Literature DB >> 25211512

Measuring genetic interactions in human cells by RNAi and imaging.

Christina Laufer1, Bernd Fischer2, Wolfgang Huber2, Michael Boutros1.   

Abstract

Observation of how genetic interactions modulate phenotypes is a powerful method for dissecting their underlying molecular and functional networks. Whereas in model organisms genetic interaction studies are well established, systematic analysis of genetic interactions in human cells has remained challenging. Here we provide a detailed protocol for large-scale mapping of genetic interactions in human cells using a high-throughput phenotyping approach. Pairwise gene product depletion is induced by siRNA-mediated knockdown, and the resulting phenotypes are quantified by automated imaging and computational analysis to provide the basis for detecting genetic interactions between all pairs of genes tested. The whole workflow, depending on the size of the experiment, takes 3 or more weeks to complete.

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Year:  2014        PMID： 25211512     DOI： 10.1038/nprot.2014.160

Source DB:  PubMed          Journal:  Nat Protoc        ISSN： 1750-2799            Impact factor:   13.491


  19 in total

1.  Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.

Authors:  Anastasia Baryshnikova; Michael Costanzo; Yungil Kim; Huiming Ding; Judice Koh; Kiana Toufighi; Ji-Young Youn; Jiongwen Ou; Bryan-Joseph San Luis; Sunayan Bandyopadhyay; Matthew Hibbs; David Hess; Anne-Claude Gingras; Gary D Bader; Olga G Troyanskaya; Grant W Brown; Brenda Andrews; Charles Boone; Chad L Myers
Journal:  Nat Methods       Date:  2010-11-14       Impact factor: 28.547

2.  Phenotypic landscape of a bacterial cell.

Authors:  Robert J Nichols; Saunak Sen; Yoe Jin Choo; Pedro Beltrao; Matylda Zietek; Rachna Chaba; Sueyoung Lee; Krystyna M Kazmierczak; Karis J Lee; Angela Wong; Michael Shales; Susan Lovett; Malcolm E Winkler; Nevan J Krogan; Athanasios Typas; Carol A Gross
Journal:  Cell       Date:  2010-12-23       Impact factor: 41.582

3.  Mapping of signaling networks through synthetic genetic interaction analysis by RNAi.

Authors:  Thomas Horn; Thomas Sandmann; Bernd Fischer; Elin Axelsson; Wolfgang Huber; Michael Boutros
Journal:  Nat Methods       Date:  2011-03-06       Impact factor: 28.547

4.  Scaling up the systematic hunt for mammalian genetic interactions.

Authors:  Traver Hart; Jason Moffat
Journal:  Nat Methods       Date:  2013-05       Impact factor: 28.547

5.  Clustering phenotype populations by genome-wide RNAi and multiparametric imaging.

Authors:  Florian Fuchs; Gregoire Pau; Dominique Kranz; Oleg Sklyar; Christoph Budjan; Sandra Steinbrink; Thomas Horn; Angelika Pedal; Wolfgang Huber; Michael Boutros
Journal:  Mol Syst Biol       Date:  2010-06-08       Impact factor: 11.429

Review 6.  Systematic mapping of genetic interaction networks.

Authors:  Scott J Dixon; Michael Costanzo; Anastasia Baryshnikova; Brenda Andrews; Charles Boone
Journal:  Annu Rev Genet       Date:  2009       Impact factor: 16.830

7.  The genetic landscape of a cell.

Authors:  Michael Costanzo; Anastasia Baryshnikova; Jeremy Bellay; Yungil Kim; Eric D Spear; Carolyn S Sevier; Huiming Ding; Judice L Y Koh; Kiana Toufighi; Sara Mostafavi; Jeany Prinz; Robert P St Onge; Benjamin VanderSluis; Taras Makhnevych; Franco J Vizeacoumar; Solmaz Alizadeh; Sondra Bahr; Renee L Brost; Yiqun Chen; Murat Cokol; Raamesh Deshpande; Zhijian Li; Zhen-Yuan Lin; Wendy Liang; Michaela Marback; Jadine Paw; Bryan-Joseph San Luis; Ermira Shuteriqi; Amy Hin Yan Tong; Nydia van Dyk; Iain M Wallace; Joseph A Whitney; Matthew T Weirauch; Guoqing Zhong; Hongwei Zhu; Walid A Houry; Michael Brudno; Sasan Ragibizadeh; Balázs Papp; Csaba Pál; Frederick P Roth; Guri Giaever; Corey Nislow; Olga G Troyanskaya; Howard Bussey; Gary D Bader; Anne-Claude Gingras; Quaid D Morris; Philip M Kim; Chris A Kaiser; Chad L Myers; Brenda J Andrews; Charles Boone
Journal:  Science       Date:  2010-01-22       Impact factor: 47.728

8.  Bioconductor: open software development for computational biology and bioinformatics.

Authors:  Robert C Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Marcel Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael Irizarry; Friedrich Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang
Journal:  Genome Biol       Date:  2004-09-15       Impact factor: 13.583

9.  Quantitative genetic-interaction mapping in mammalian cells.

Authors:  Assen Roguev; Dale Talbot; Gian Luca Negri; Michael Shales; Gerard Cagney; Sourav Bandyopadhyay; Barbara Panning; Nevan J Krogan
Journal:  Nat Methods       Date:  2013-02-13       Impact factor: 28.547

10.  A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility.

Authors:  Michael C Bassik; Martin Kampmann; Robert Jan Lebbink; Shuyi Wang; Marco Y Hein; Ina Poser; Jimena Weibezahn; Max A Horlbeck; Siyuan Chen; Matthias Mann; Anthony A Hyman; Emily M Leproust; Michael T McManus; Jonathan S Weissman
Journal:  Cell       Date:  2013-02-08       Impact factor: 41.582
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  9 in total

Review 1.  Systems medicine: evolution of systems biology from bench to bedside.

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Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2015-04-17

2.  Capturing Single-Cell Phenotypic Variation via Unsupervised Representation Learning.

Authors:  Maxime W Lafarge; Juan C Caicedo; Anne E Carpenter; Josien P W Pluim; Shantanu Singh; Mitko Veta
Journal:  Proc Mach Learn Res       Date:  2019-07

3.  A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay.

Authors:  Antoine-Emmanuel Saliba; Ivana Vonkova; Samy Deghou; Stefano Ceschia; Christian Tischer; Karl G Kugler; Peer Bork; Jan Ellenberg; Anne-Claude Gavin
Journal:  Nat Protoc       Date:  2016-05-05       Impact factor: 13.491

Review 4.  The systematic analysis of protein-lipid interactions comes of age.

Authors:  Antoine-Emmanuel Saliba; Ivana Vonkova; Anne-Claude Gavin
Journal:  Nat Rev Mol Cell Biol       Date:  2015-10-28       Impact factor: 94.444

5.  The Deubiquitinase USP47 Stabilizes MAPK by Counteracting the Function of the N-end Rule ligase POE/UBR4 in Drosophila.

Authors:  Dariel Ashton-Beaucage; Caroline Lemieux; Christian M Udell; Malha Sahmi; Samuel Rochette; Marc Therrien
Journal:  PLoS Biol       Date:  2016-08-23       Impact factor: 8.029

6.  Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae.

Authors:  Dimitris Kyriakou; Emmanouil Stavrou; Panayiota Demosthenous; Georgia Angelidou; Bryan-Joseph San Luis; Charles Boone; Vasilis J Promponas; Antonis Kirmizis
Journal:  BMC Biol       Date:  2016-12-07       Impact factor: 7.431

Review 7.  Prediction of Genetic Interactions Using Machine Learning and Network Properties.

Authors:  Neel S Madhukar; Olivier Elemento; Gaurav Pandey
Journal:  Front Bioeng Biotechnol       Date:  2015-10-26

8.  Metformin inhibits pancreatic cancer metastasis caused by SMAD4 deficiency and consequent HNF4G upregulation.

Authors:  Dongxin Lin; Chen Wu; Yupei Zhao; Chengcheng Wang; Taiping Zhang; Quan Liao; Menghua Dai; Junchao Guo; Xinyu Yang; Wen Tan
Journal:  Protein Cell       Date:  2020-07-31       Impact factor: 14.870

9.  A high-content platform to characterise human induced pluripotent stem cell lines.

Authors:  Andreas Leha; Nathalie Moens; Ruta Meleckyte; Oliver J Culley; Mia K Gervasio; Maximilian Kerz; Andreas Reimer; Stuart A Cain; Ian Streeter; Amos Folarin; Oliver Stegle; Cay M Kielty; Richard Durbin; Fiona M Watt; Davide Danovi
Journal:  Methods       Date:  2015-11-25       Impact factor: 3.608
  9 in total

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