Contemporary, yeast-based approaches to understanding human genetic variation

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Determining how genetic variation contributes to human health and disease is a critical challenge. As one of the most genetically tractable model organisms, yeast has played a central role in meeting this challenge. The advent of new technologies, including high-throughput DNA sequencing and synthesis, proteomics, and computational methods, has vastly increased the power of yeast-based approaches to determine the consequences of human genetic variation. Recent successes include systematic exploration of the effects of gene dosage, large-scale analysis of the effect of coding variation on gene function, and the use of humanized yeast to model disease. By virtue of its manipulability, small genome size, and genetic tractability, yeast is poised to help us understand human genetic variation.

Introduction

With acceleration of sequencing technologies, many human genomes are becoming available from patients, tumors, and thousands of individuals from diverse populations. In parallel, linkage mapping, genome-wide association strategies, and analyses of de novo mutations are rapidly linking genomic regions to phenotypes including disease susceptibility. However, defining which genetic variants are causative for phenotype has become rate-limiting. Furthermore, the abundance of rare variation means that sequencing more genomes is unlikely to solve this problem (e.g. [1, 2]). We propose that new technologies such as high-throughput DNA sequencing, proteomics, and computational approaches can empower model organism genetics to fill this gap by enabling high-throughput, generic, genome-scale functional assays for characterizing variation in the human genome. Yeast, especially the budding yeast S. cerevisiae, is uniquely suited to this task because of its versatility, small genome size, and powerful array of existing tools (reviewed in [3]). Methods for understanding the consequences of human variation using yeast fall into three broad categories: 1. systematic analysis of gene dosage; 2. recreation of human variants in their yeast orthologs; and 3. cross-species complementation and heterologous expression. In addition to enabling direct measurement of the consequences of specific genetic variants, work in yeast and other model organisms will be necessary for understanding the essential underlying biology. These larger biological questions include the distribution of effect sizes of genetic variants, the contribution of genetic modifiers and the role of epistasis more generally, and, of course, the fundamental molecular mechanisms by which genes and their variants act.

Section snippets

Systematic analysis of gene dosage

Yeast is easily amenable to purposeful manipulation of gene dosage, most frequently via loss of function but increasingly by overexpression as well. Examining the resulting phenotypes can reveal the function of the element whose dosage is changed (Figure 1a). When specific phenotypes are shared, connections between yeast and human can be relatively easy to recognize. Famously, work in yeast correctly predicted the role of the human mismatch repair genes hPMS1, hMLH1, and hMSH2 in hereditary

Recreation of genetic variants in orthologs

Complete loss-of-function alleles comprise a minority of the relevant genetic variation in humans and other organisms. Most genes have many alleles ranging from complete loss of function to subtle alterations in function. For genomic regions with significant conservation, human variants can be tested for function by making homologous mutations in their yeast orthologs (Figure 1b). For example, MSH2 alleles associated with hereditary colon cancer were systematically evaluated in yeast, where

Cross-species complementation and heterologous expression

Despite the value of using orthologous genes, conservation-based inference of mutation effects can be fraught [35]. In some cases, direct testing of variants in their native gene context might be more desirable. In yeast, this has been attempted in two ways: cross-species complementation and heterologous expression. Cross-species complementation is simply the ability of human genes to rescue an orthologous loss-of-function mutation in another organism (Figure 1c). The conservation of core cell

Limitations of model organism approaches

Of course, all model systems have their downsides. Approaches in yeast might be most productively viewed as a method for intelligently prioritizing experiments to be done in more complicated and expensive mammalian models. An obvious caveat of evaluating human alleles in other organisms is that some genes will not be equivalently functional outside their native context of a human cell. Furthermore, some variants may disrupt interactions with proteins not present or too diverged in other

Conclusion

We have argued that yeast is an ideal model organism in which to address the consequences of human genomic variation. We have reviewed the key approaches that have already allowed huge progress in understanding human and yeast genetic perturbations, ranging from single point mutations to entire extra chromosomes. Additionally, the genetics underlying disease is sometimes so poorly understood that model organisms are needed just to define these basics (reviewed in [61]). For example, complex

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

MD is a Rita Allen Foundation Scholar and a Canadian Institute for Advanced Research Fellow. She is supported by grants from the National Institute of General Medical Sciences (P41 GM103533, R01GM094306 and R01GM101091) from the National Institutes of Health.

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