Genetic interactions reveal the evolutionary trajectories of duplicate genes.
Benjamin VanderSluis,Jeremy Bellay,Gabriel Musso,Michael Costanzo,Balázs Papp,Franco J. Vizeacoumar,Anastasia Baryshnikova,Brenda J. Andrews,Charles Boone,Chad L. Myers +9 more
TLDR
It is shown that duplicate genes exhibit fewer genetic interactions than other genes because they tend to buffer one another functionally, whereas observed interactions are non‐overlapping and reflect their divergent roles.Abstract:
The characterization of functional redundancy and divergence between duplicate genes is an important step in understanding the evolution of genetic systems. Large-scale genetic network analysis in Saccharomyces cerevisiae provides a powerful perspective for addressing these questions through quantitative measurements of genetic interactions between pairs of duplicated genes, and more generally, through the study of genome-wide genetic interaction profiles associated with duplicated genes. We show that duplicate genes exhibit fewer genetic interactions than other genes because they tend to buffer one another functionally, whereas observed interactions are non-overlapping and reflect their divergent roles. We also show that duplicate gene pairs are highly imbalanced in their number of genetic interactions with other genes, a pattern that appears to result from asymmetric evolution, such that one duplicate evolves or degrades faster than the other and often becomes functionally or conditionally specialized. The differences in genetic interactions are predictive of differences in several other evolutionary and physiological properties of duplicate pairs.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.
Journal ArticleDOI
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
TL;DR: It is proposed that the universal bias in gene loss between the genomes of this ancient tetraploid, and perhaps all tetraPLoids, is the result of selection against loss of the gene responsible for the majority of total expression for a duplicate gene pair.
Journal ArticleDOI
Molecular mechanisms of epistasis within and between genes
TL;DR: An overview of the current understanding of the molecular mechanisms that can cause epistasis, and areas where more research is needed are provided.
Journal ArticleDOI
Systematic analysis of complex genetic interactions
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 A. Caudy,Daniel I. Bolnick,Grant W. Brown,Brenda J. Andrews,Charles Boone,Chad L. Myers +31 more
TL;DR: The extensive network of trigenic interactions and their ability to generate functionally diverse phenotypes suggest that higher-order genetic interactions may play a key role in the genotype-to-phenotype relationship, genome size, and speciation.
Journal ArticleDOI
Genome and gene duplications and gene expression divergence: a view from plants
TL;DR: Following various mechanisms of gene duplication, genes are often retained or lost in a biased manner, which has suggested recent models for gene family evolution, such as functional buffering and the gene balance hypothesis in addition to now‐classical models, including neofunctionalization and subfunctionalization.
References
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Journal Article
Preservation of duplicate genes by complementary, degenerative mutations.
TL;DR: Cooke et al. as mentioned in this paper proposed a new conceptual framework for understanding the evolution of duplicate genes that may help explain this conundrum, focusing on the regulatory complexity of eukaryotic genes, and showed how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the development of new gene functions.
Journal ArticleDOI
Preservation of Duplicate Genes by Complementary, Degenerative Mutations
TL;DR: Focusing on the regulatory complexity of eukaryotic genes, it is shown how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions.
Journal ArticleDOI
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Nevan J. Krogan,Gerard Cagney,Gerard Cagney,Haiyuan Yu,Gouqing Zhong,Xinghua Guo,Alexandr Ignatchenko,Joyce Li,Shuye Pu,Nira Datta,Aaron 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 Richards,Veronica Canadien,Atanas Iliev Lalev,Frank Mena,Peter D 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 K. O'Shea,Jonathan S. Weissman,C. James Ingles,Timothy P. Hughes,John Parkinson,Mark Gerstein,Shoshana J. Wodak,Andrew Emili,Jack Greenblatt +53 more
TL;DR: T tandem affinity purification was used to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae to identify protein–protein interactions, which will help future studies on individual proteins as well as functional genomics and systems biology.
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NCBI BLAST: a better web interface
Mark D. Johnson,Irena Zaretskaya,Yan Raytselis,Yuri Merezhuk,Scott D. McGinnis,Thomas L. Madden +5 more
TL;DR: The public interface of BLAST at the NCBI website has recently been reengineered to improve usability and performance, and key new features include simplified search forms, improved navigation, and a list of recent BLAST results.
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