Literature DB >> 23746449

Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation.

James E Haber1, Hannes Braberg, Qiuqin Wu, Richard Alexander, Julian Haase, Colm Ryan, Zach Lipkin-Moore, Kathleen E Franks-Skiba, Tasha Johnson, Michael Shales, Tineke L Lenstra, Frank C P Holstege, Jeffrey R Johnson, Kerry Bloom, Nevan J Krogan.   

Abstract

Genetic interactions reveal the functional relationships between pairs of genes. In this study, we describe a method for the systematic generation and quantitation of triple mutants, termed triple-mutant analysis (TMA). We have used this approach to interrogate partially redundant pairs of genes in S. cerevisiae, including ASF1 and CAC1, two histone chaperones. After subjecting asf1Δ cac1Δ to TMA, we found that the Swi/Snf Rdh54 protein compensates for the absence of Asf1 and Cac1. Rdh54 more strongly associates with the chromatin apparatus and the pericentromeric region in the double mutant. Moreover, Asf1 is responsible for the synthetic lethality observed in cac1Δ strains lacking the HIRA-like proteins. A similar TMA was carried out after deleting both CLB5 and CLB6, cyclins that regulate DNA replication, revealing a strong functional connection to chromosome segregation. This approach can reveal functional redundancies that cannot be uncovered through traditional double-mutant analyses.
Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

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Year:  2013        PMID: 23746449      PMCID: PMC3718395          DOI: 10.1016/j.celrep.2013.05.007

Source DB:  PubMed          Journal:  Cell Rep            Impact factor:   9.423


  77 in total

1.  Diverse functions of spindle assembly checkpoint genes in Saccharomyces cerevisiae.

Authors:  Jewel A Daniel; Brice E Keyes; Yvonne P Y Ng; C Onyi Freeman; Daniel J Burke
Journal:  Genetics       Date:  2005-09-12       Impact factor: 4.562

2.  Replication-independent histone deposition by the HIR complex and Asf1.

Authors:  Erin M Green; Andrew J Antczak; Aaron O Bailey; Alexa A Franco; Kevin J Wu; John R Yates; Paul D Kaufman
Journal:  Curr Biol       Date:  2005-11-22       Impact factor: 10.834

3.  Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile.

Authors:  Maya Schuldiner; Sean R Collins; Natalie J Thompson; Vladimir Denic; Arunashree Bhamidipati; Thanuja Punna; Jan Ihmels; Brenda Andrews; Charles Boone; Jack F Greenblatt; Jonathan S Weissman; Nevan J Krogan
Journal:  Cell       Date:  2005-11-04       Impact factor: 41.582

4.  The Tof1p-Csm3p protein complex counteracts the Rrm3p helicase to control replication termination of Saccharomyces cerevisiae.

Authors:  Bidyut K Mohanty; Narendra K Bairwa; Deepak Bastia
Journal:  Proc Natl Acad Sci U S A       Date:  2006-01-17       Impact factor: 11.205

5.  Checkpoint functions are required for normal S-phase progression in Saccharomyces cerevisiae RCAF- and CAF-I-defective mutants.

Authors:  Ellen S Kats; Claudio P Albuquerque; Huilin Zhou; Richard D Kolodner
Journal:  Proc Natl Acad Sci U S A       Date:  2006-02-24       Impact factor: 11.205

6.  Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions.

Authors:  M Schuldiner; S R Collins; J S Weissman; N J Krogan
Journal:  Methods       Date:  2006-12       Impact factor: 3.608

7.  Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways.

Authors:  Ben Lehner; Catriona Crombie; Julia Tischler; Angelo Fortunato; Andrew G Fraser
Journal:  Nat Genet       Date:  2006-07-16       Impact factor: 38.330

8.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Authors:  Nevan J Krogan; Gerard Cagney; Haiyuan Yu; Gouqing Zhong; Xinghua Guo; Alexandr Ignatchenko; Joyce Li; Shuye Pu; Nira Datta; Aaron P Tikuisis; Thanuja Punna; José M Peregrín-Alvarez; Michael Shales; Xin Zhang; Michael Davey; Mark D Robinson; Alberto Paccanaro; James E Bray; Anthony Sheung; Bryan Beattie; Dawn P Richards; Veronica Canadien; Atanas Lalev; Frank Mena; Peter Wong; Andrei Starostine; Myra M Canete; James Vlasblom; Samuel Wu; Chris Orsi; Sean R Collins; Shamanta Chandran; Robin Haw; Jennifer J Rilstone; Kiran Gandi; Natalie J Thompson; Gabe Musso; Peter St Onge; Shaun Ghanny; Mandy H Y Lam; Gareth Butland; Amin M Altaf-Ul; Shigehiko Kanaya; Ali Shilatifard; Erin O'Shea; Jonathan S Weissman; C James Ingles; Timothy R Hughes; John Parkinson; Mark Gerstein; Shoshana J Wodak; Andrew Emili; Jack F Greenblatt
Journal:  Nature       Date:  2006-03-22       Impact factor: 49.962

9.  Activation of the DNA damage checkpoint in yeast lacking the histone chaperone anti-silencing function 1.

Authors:  Christopher Josh Ramey; Susan Howar; Melissa Adkins; Jeffrey Linger; Judson Spicer; Jessica K Tyler
Journal:  Mol Cell Biol       Date:  2004-12       Impact factor: 4.272

10.  Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56.

Authors:  Robert Driscoll; Amanda Hudson; Stephen P Jackson
Journal:  Science       Date:  2007-02-02       Impact factor: 47.728

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  25 in total

1.  Mapping a diversity of genetic interactions in yeast.

Authors:  Jolanda van Leeuwen; Charles Boone; Brenda J Andrews
Journal:  Curr Opin Syst Biol       Date:  2017-08-12

2.  Replisome function during replicative stress is modulated by histone h3 lysine 56 acetylation through Ctf4.

Authors:  Pierre Luciano; Pierre-Marie Dehé; Stéphane Audebert; Vincent Géli; Yves Corda
Journal:  Genetics       Date:  2015-02-18       Impact factor: 4.562

3.  A genetic approach to study polyubiquitination in Saccharomyces cerevisiae.

Authors:  Fernando Meza-Gutierrez; Deniz Simsek; David Paul Toczyski
Journal:  Methods Enzymol       Date:  2019-02-21       Impact factor: 1.600

4.  Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments.

Authors:  Philipp A Jaeger; Cameron McElfresh; Lily R Wong; Trey Ideker
Journal:  Appl Environ Microbiol       Date:  2015-06-12       Impact factor: 4.792

5.  Systematic analysis of complex genetic interactions.

Authors:  Elena Kuzmin; Benjamin VanderSluis; Wen Wang; Guihong Tan; Raamesh Deshpande; Yiqun Chen; Matej Usaj; Attila Balint; Mojca Mattiazzi Usaj; Jolanda van Leeuwen; Elizabeth N Koch; Carles Pons; Andrius J Dagilis; Michael Pryszlak; Jason Zi Yang Wang; Julia Hanchard; Margot Riggi; Kaicong Xu; Hamed Heydari; Bryan-Joseph San Luis; Ermira Shuteriqi; Hongwei Zhu; Nydia Van Dyk; Sara Sharifpoor; Michael Costanzo; Robbie Loewith; Amy Caudy; Daniel Bolnick; Grant W Brown; Brenda J Andrews; Charles Boone; Chad L Myers
Journal:  Science       Date:  2018-04-20       Impact factor: 47.728

Review 6.  Histone chaperone CAF-1: essential roles in multi-cellular organism development.

Authors:  Zhongsheng Yu; Jiyong Liu; Wu-Min Deng; Renjie Jiao
Journal:  Cell Mol Life Sci       Date:  2014-10-08       Impact factor: 9.261

7.  Genetic interaction mapping informs integrative structure determination of protein complexes.

Authors:  Hannes Braberg; Ignacia Echeverria; Stefan Bohn; Peter Cimermancic; Anthony Shiver; Richard Alexander; Jiewei Xu; Michael Shales; Raghuvar Dronamraju; Shuangying Jiang; Gajendradhar Dwivedi; Derek Bogdanoff; Kaitlin K Chaung; Ruth Hüttenhain; Shuyi Wang; David Mavor; Riccardo Pellarin; Dina Schneidman; Joel S Bader; James S Fraser; John Morris; James E Haber; Brian D Strahl; Carol A Gross; Junbiao Dai; Jef D Boeke; Andrej Sali; Nevan J Krogan
Journal:  Science       Date:  2020-12-11       Impact factor: 47.728

Review 8.  Global Genetic Networks and the Genotype-to-Phenotype Relationship.

Authors:  Michael Costanzo; Elena Kuzmin; Jolanda van Leeuwen; Barbara Mair; Jason Moffat; Charles Boone; Brenda Andrews
Journal:  Cell       Date:  2019-03-21       Impact factor: 41.582

Review 9.  High-resolution network biology: connecting sequence with function.

Authors:  Colm J Ryan; Peter Cimermančič; Zachary A Szpiech; Andrej Sali; Ryan D Hernandez; Nevan J Krogan
Journal:  Nat Rev Genet       Date:  2013-11-07       Impact factor: 53.242

10.  Quantitative analysis of triple-mutant genetic interactions.

Authors:  Hannes Braberg; Richard Alexander; Michael Shales; Jiewei Xu; Kathleen E Franks-Skiba; Qiuqin Wu; James E Haber; Nevan J Krogan
Journal:  Nat Protoc       Date:  2014-07-10       Impact factor: 13.491

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