Phenomics Approaches to Understand Genetic Networks and Gene Function in Yeast

Overview

Journal Biochem Soc Trans

Specialty Biochemistry

Date 2022 Mar 14

PMID 35285506

Authors

Clarence Hue Lok Yeung

Nil Sahin

Brenda Andrews

Affiliations

Soon will be listed here.

Abstract

Over the past decade, major efforts have been made to systematically survey the characteristics or phenotypes associated with genetic variation in a variety of model systems. These so-called phenomics projects involve the measurement of 'phenomes', or the set of phenotypic information that describes an organism or cell, in various genetic contexts or states, and in response to external factors, such as environmental signals. Our understanding of the phenome of an organism depends on the availability of reagents that enable systematic evaluation of the spectrum of possible phenotypic variation and the types of measurements that can be taken. Here, we highlight phenomics studies that use the budding yeast, a pioneer model organism for functional genomics research. We focus on genetic perturbation screens designed to explore genetic interactions, using a variety of phenotypic read-outs, from cell growth to subcellular morphology.

Citing Articles

Cancer phenomics research hotspots and development trends: a bibliometric analysis from 2000 to 2023.

Chen S, Liu J, Tang N, Zeng Y Discov Oncol. 2024; 15(1):811.

PMID: 39695032 PMC: 11655722. DOI: 10.1007/s12672-024-01710-w.

Multi-Attribute Subset Selection enables prediction of representative phenotypes across microbial populations.

Herbst K, Wang T, Forchielli E, Thommes M, Paschalidis I, Segre D Commun Biol. 2024; 7(1):407.

PMID: 38570615 PMC: 10991586. DOI: 10.1038/s42003-024-06093-w.

Automated quantification of vacuole fusion and lipophagy in from fluorescence and cryo-soft X-ray microscopy data using deep learning.

Egebjerg J, Szomek M, Thaysen K, Juhl A, Kozakijevic S, Werner S Autophagy. 2023; 20(4):902-922.

PMID: 37908116 PMC: 11062380. DOI: 10.1080/15548627.2023.2270378.

Genomic Adaptations of Genus to Wine Niche.

Garcia-Rios E, Guillamon J Microorganisms. 2022; 10(9).

PMID: 36144411 PMC: 9500811. DOI: 10.3390/microorganisms10091811.

References

Li Z, Vizeacoumar F, Bahr S, Li J, Warringer J, Vizeacoumar F . Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat Biotechnol. 2011; 29(4):361-7. PMC: 3286520. DOI: 10.1038/nbt.1832. View

Breslow D, Cameron D, Collins S, Schuldiner M, Stewart-Ornstein J, Newman H . A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods. 2008; 5(8):711-8. PMC: 2756093. DOI: 10.1038/nmeth.1234. View

Sanders E, Nguyen P, Rogers C, Bochman M . Comprehensive Synthetic Genetic Array Analysis of Alleles That Interact with Mutation of the RecQ Helicases Hrq1 and Sgs1. G3 (Bethesda). 2020; 10(12):4359-4368. PMC: 7718751. DOI: 10.1534/g3.120.401709. View

Collins S, Schuldiner M, Krogan N, Weissman J . A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol. 2006; 7(7):R63. PMC: 1779568. DOI: 10.1186/gb-2006-7-7-r63. View

Houle D, Govindaraju D, Omholt S . Phenomics: the next challenge. Nat Rev Genet. 2010; 11(12):855-66. DOI: 10.1038/nrg2897. View

Yofe I, Weill U, Meurer M, Chuartzman S, Zalckvar E, Goldman O . One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy. Nat Methods. 2016; 13(4):371-378. PMC: 4869835. DOI: 10.1038/nmeth.3795. View

Costanzo M, Kuzmin E, van Leeuwen J, Mair B, Moffat J, Boone C . Global Genetic Networks and the Genotype-to-Phenotype Relationship. Cell. 2019; 177(1):85-100. PMC: 6817365. DOI: 10.1016/j.cell.2019.01.033. View

Hanna R, Doench J . Design and analysis of CRISPR-Cas experiments. Nat Biotechnol. 2020; 38(7):813-823. DOI: 10.1038/s41587-020-0490-7. View

Pan X, Yuan D, Ooi S, Wang X, Sookhai-Mahadeo S, Meluh P . dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae. Methods. 2006; 41(2):206-21. PMC: 2491713. DOI: 10.1016/j.ymeth.2006.07.033. View

10.

Grys B, Lo D, Sahin N, Kraus O, Morris Q, Boone C . Machine learning and computer vision approaches for phenotypic profiling. J Cell Biol. 2016; 216(1):65-71. PMC: 5223612. DOI: 10.1083/jcb.201610026. View

11.

Mattiazzi Usaj M, Sahin N, Friesen H, Pons C, Usaj M, Masinas M . Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability. Mol Syst Biol. 2020; 16(2):e9243. PMC: 7025093. DOI: 10.15252/msb.20199243. View

12.

Haber J, Braberg H, Wu Q, Alexander R, Haase J, Ryan C . Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation. Cell Rep. 2013; 3(6):2168-78. PMC: 3718395. DOI: 10.1016/j.celrep.2013.05.007. View

13.

Lehner B . Genotype to phenotype: lessons from model organisms for human genetics. Nat Rev Genet. 2013; 14(3):168-78. DOI: 10.1038/nrg3404. View

14.

Schuldiner M, Collins S, Thompson N, Denic V, Bhamidipati A, Punna T . Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell. 2005; 123(3):507-19. DOI: 10.1016/j.cell.2005.08.031. View

15.

Huh W, Falvo J, Gerke L, Carroll A, Howson R, Weissman J . Global analysis of protein localization in budding yeast. Nature. 2003; 425(6959):686-91. DOI: 10.1038/nature02026. View

16.

Weill U, Yofe I, Sass E, Stynen B, Davidi D, Natarajan J . Genome-wide SWAp-Tag yeast libraries for proteome exploration. Nat Methods. 2018; 15(8):617-622. PMC: 6076999. DOI: 10.1038/s41592-018-0044-9. View

17.

Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear E, Sevier C . The genetic landscape of a cell. Science. 2010; 327(5964):425-31. PMC: 5600254. DOI: 10.1126/science.1180823. View

18.

Mattiazzi Usaj M, Yeung C, Friesen H, Boone C, Andrews B . Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations. Cell Syst. 2021; 12(6):608-621. PMC: 9112900. DOI: 10.1016/j.cels.2021.05.010. View

19.

Weill U, Krieger G, Avihou Z, Milo R, Schuldiner M, Davidi D . Assessment of GFP Tag Position on Protein Localization and Growth Fitness in Yeast. J Mol Biol. 2018; 431(3):636-641. PMC: 7611381. DOI: 10.1016/j.jmb.2018.12.004. View

20.

Witkin K, Chong Y, Shao S, Webster M, Lahiri S, Walters A . The budding yeast nuclear envelope adjacent to the nucleolus serves as a membrane sink during mitotic delay. Curr Biol. 2012; 22(12):1128-33. PMC: 3381997. DOI: 10.1016/j.cub.2012.04.022. View