Skip to main content Accessibility help
×
Home
  • Print publication year: 2015
  • Online publication date: July 2015

3 - Mapping genetic interactions across many phenotypes in metazoan cells

Summary

Interactions between genes can be experimentally determined by combining multiple mutations and identifying combinations where the resulting phenotype differs from the expected one. Such genetic interactions, for example measured in yeast for cell proliferation and growth phenotypes, provided intricate insights into the genetic architecture and interplay of pathways. Due to the lack of comprehensive deletion libraries, similar experiments in higher eukaryotic cells have been challenging. Recently, we and others described methods to perform systematic, comprehensive double-perturbation analyses in Drosophila and human cells using RNA interference. We also introduced methods to use multiple phenotypes to map genetic interactions across a broad spectrum of processes.

This chapter focuses on the systematic mapping of genetic interactions and the use of image-based phenotypes to improve genetic interaction calling. It also describes experimental approaches for the analysis of genetic interactions in human cells and discusses concepts to expand genetic interaction mapping towards a genomic scale.

A short history of genetic interaction analysis

Using quantitative traits to map genetic interactions has a long tradition in Drosophila. In the 1960s and 1970s, Dobzhansky, Rendel, and others used externally visible pheno-types or overall fitness to study non-mendelian inheritance and dissect the heritability of complex traits (Fig. 3.1a). One of the underlying assumptions was that genetic loci in the Drosophila genome interact to shape complex phenotypes or buffer detrimental alleles.

In 1965, Dobzhansky and colleagues analyzed epistatic interactions between the components of genetic variants in Drosophila. They crossed flies carrying mutant alleles into a wild-type background obtained from a natural habitat and found that the combination of particular chromosomes showed synthetic sick phenotypes, whereas both chromosomes alone did not. This for the first time demonstrated the presence of bi-chromosomal synthetic interactions in Drosophila populations. Similarly, Rendel and colleagues demonstrated the existence of epistatic modifiers in Drosophila by analysis of scute alleles, which reduce the number of scutellar bristles on the dorsal thorax from four to an average of one.

Axelsson, E., Sandmann, T., Horn, T., Boutros, M., Huber, W., et al. (2011), ‘Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAI’, BMC Bioinformatics 12, 342.
Bakal, C., Linding, R., Llense, F., Heffern, E., Martin-Blanco, E., et al. (2008), ‘Phosphorylation networks regulating jnk activity in diverse genetic backgrounds’, Science 322(5900), 453–6.
Bartscherer, K., Pelte, N., Ingelfinger, D., & Boutros, M., (2006), ‘Secretion of wnt ligands requires evi, a conserved transmembrane protein’, Cell 125 (3), 523–33.
Bassik, M. C., Kampmann, M., Lebbink, R. J., Wang, S., Hein, M. Y. et al. (2013), ‘A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility’, Cell 152 (4), 909–22.
Ben-Aroya, S., Coombes, C., Kwok, T., O'Donnell, K. A., Boeke, J. D. et al. (2008), ‘Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae’, Mol Cell 30 (2), 248–58.
Björklund, M., Taipale, M., Varjosalo, M., Saharinen, J., Lahdenperä, J. et al. (2006), ‘Identification of pathways regulating cell size and cell-cycle progression by RNAI’, Nature 439(7079), 1009–13.
Boutros, M., Kiger, A. A., Armknecht, S., Kerr, K., Hild, M., et al. (2004), ‘Genome-wide rnai analysis of growth and viability in Drosophila cells’, Science 303(5659), 832–5.
Carter, G. W. (2013), ‘Inferring gene function and network organization in Drosophila signaling by combined analysis of pleiotropy and epistasis’, G3 (Bethesda) 3 (5), 807–14.
Casey, F. P., Cagney, G., Krogan, N. J. & Shields, D. C. (2008), ‘Optimal stepwise experimental design for pairwise functional interaction studies’, Bioinformatics 24 (23), 2733–9.
Collins, S. R.,Miller, K. M.,Maas, N. L., Roguev, A., Fillingham, J., et al. (2007), ‘Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map’, Nature 446(7137), 806–10.
Collins, S. R., Roguev, A., & Krogan, N. J. (2010), ‘Quantitative genetic interaction mapping using the E-MAP approach’, Methods Enzymol 470, 205–31.
Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D. et al. (2010), ‘The genetic landscape of a cell’, Science 327(5964), 425–31.
Dixon, S. J., Costanzo, M., Baryshnikova, A., Andrews, B., & Boone, C., (2009), ‘Systematic mapping of genetic interaction networks’, Annu Rev Genet 43, 601–25.
Friedman, A., & Perrimon, N., (2006), ‘A functional RNAI screen for regulators of receptor tyrosine kinase and ERK signalling’, Nature 444(7116), 230–4.
Horn, T., Sandmann, T., Fischer, B., Axelsson, E., Huber, W., et al. (2011), ‘Mapping of signaling networks through synthetic genetic interaction analysis by RNAI’, Nat Methods 8 (4), 341–6.
Kampmann, M., Bassik, M. C. & Weissman, J. S. (2013), ‘Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells’, Proc Natl Acad Sci U S A 110 (25), E2317–26.
Kittler, R., Surendranath, V., Heninger, A. -K.Slabicki, M., Theis, M., et al. (2007), ‘Genome-wide resources of endoribonuclease-prepared short interfering RNAS for specific loss-of-function studies’, Nat Methods 4 (4), 337–44.
Kuzmin, E., Sharifpoor, S., Baryshnikova, A., Costanzo, M., Myers, C. L. et al. (2014), ‘Synthetic genetic array analysis for global mapping of genetic networks in yeast’, Methods Mol Biol 1205, 143–68.
Laufer, C., Fischer, B., Billmann, M., Huber, W., & Boutros, M., (2013), ‘Mapping genetic interactions in human cancer cells with RNAI and multiparametric phenotyping’, Nat Methods 10 (5), 427–31.
Laufer, C., Fischer, B., Huber,W. &Boutros, M., (2014), ‘Measuring genetic interactions in human cells by RNAI and imaging’, Nat Protoc 9 (10), 2341–53.
Müller, P., Kuttenkeuler, D., Gesellchen, V., Zeidler, M. P. & Boutros, M., (2005), ‘Identification of JAK/STAT signalling components by genome-wide RNA interference’, Nature 436(7052), 871–5.
Roguev, A., Talbot, D., Negri, G. L., Shales, M., Cagney, G., et al. (2013), ‘Quantitative geneticinteraction mapping in mammalian cells’, Nat Methods 10 (5), 432–7.
Schuldiner, M., Collins, S. R., Thompson, N. J., Denic, V., Bhamidipati, A., et al. (2005), ‘Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile’, Cell 123 (3), 507–19.
St Johnston, D., (2002), ‘The art and design of genetic screens: Drosophila melanogaster’, Nat Rev Genet 3 (3), 176–88.
Tong, A. H., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D. et al. (2001), ‘Systematic genetic analysis with ordered arrays of yeast deletion mutants’, Science 294(5550), 2364–8.
Tong, A. H. Y., Lesage, G., Bader, G. D., Ding, H., Xu, H., et al. (2004), ‘Global mapping of the yeast genetic interaction network’, Science 303(5659), 808–13.
Wassarman, D. A., Therrien, M., & Rubin, G. M. (1995), ‘The Ras signaling pathway in Drosophila’, Curr Opin Genet Dev 5 (1), 44–50.
Winzeler, E. A., Shoemaker, D. D., Astromoff, A., Liang, H., Anderson, K., et al. (1999), ‘Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis’, Science 285(5429), 901–6.