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Science (New York, N.Y.)
06 26, 2020;368 (6498):

Exploring whole-genome duplicate gene retention with complex genetic interaction analysis.

Elena Kuzmin, Benjamin VanderSluis, Alex N Nguyen Ba, Wen Wang, Elizabeth N Koch, Matej Usaj, Anton Khmelinskii, Mojca Mattiazzi Usaj, Jolanda van Leeuwen, Oren Kraus, Amy Tresenrider, Michael Pryszlak, Ming-Che Hu, Brenda Varriano, Michael Costanzo, Michael Knop, Alan Moses, Chad L Myers, Brenda J Andrews, Charles Boone
Author Information
  1. Elena Kuzmin: Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. ORCID
  2. Benjamin VanderSluis: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA. ORCID
  3. Alex N Nguyen Ba: Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada. ORCID
  4. Wen Wang: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA. ORCID
  5. Elizabeth N Koch: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
  6. Matej Usaj: Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. ORCID
  7. Anton Khmelinskii: Zentrum f��r Molekulare Biologie der Universit��t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany. ORCID
  8. Mojca Mattiazzi Usaj: Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. ORCID
  9. Jolanda van Leeuwen: Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. ORCID
  10. Oren Kraus: Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
  11. Amy Tresenrider: Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. ORCID
  12. Michael Pryszlak: Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. ORCID
  13. Ming-Che Hu: Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. ORCID
  14. Brenda Varriano: Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
  15. Michael Costanzo: Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. ORCID
  16. Michael Knop: Zentrum f��r Molekulare Biologie der Universit��t Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany. ORCID
  17. Alan Moses: Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada. ORCID
  18. Chad L Myers: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA. charlie.boone@utoronto.ca brenda.andrews@utoronto.ca chadm@umn.edu. ORCID
  19. Brenda J Andrews: Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. charlie.boone@utoronto.ca brenda.andrews@utoronto.ca chadm@umn.edu. ORCID
  20. Charles Boone: Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada. charlie.boone@utoronto.ca brenda.andrews@utoronto.ca chadm@umn.edu. ORCID
PMID: 32586993 DOI: 10.1126/science.aaz5667

Abstract

Whole-genome duplication has played a central role in the genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated, and factors that influence the retention of persisting duplicates remain poorly understood. We describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping of digenic interactions for a deletion mutant of each paralog, and of trigenic interactions for the double mutant, provides insight into their roles and a quantitative measure of their functional redundancy. Trigenic interaction analysis distinguishes two classes of paralogs: a more functionally divergent subset and another that retained more functional overlap. Gene feature analysis and modeling suggest that evolutionary trajectories of duplicated genes are dictated by combined functional and structural entanglement factors.

Associated Data

Dryad | 10.5061/dryad.g79cnp5m9

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Grants

  1. R01 GM104975/NIGMS NIH HHS
  2. R01 HG005084/NHGRI NIH HHS
  3. R01 HG005853/NHGRI NIH HHS

MeSH Term

Gene Deletion
Gene Duplication
Gene Regulatory Networks
Genes, Duplicate
Genetic Techniques
Genome, Fungal
Membrane Proteins
Peroxins
Protein Interaction Maps
Saccharomyces cerevisiae
Saccharomyces cerevisiae Proteins

Chemicals

Membrane Proteins
PEX25 protein, S cerevisiae
Peroxins
Pex27 protein, S cerevisiae
Saccharomyces cerevisiae Proteins
Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't
Article has an altmetric score of 42

Word Cloud

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