From sequence to function: Insights from natural variation in budding yeasts

Abstract

Background: Natural variation offers a powerful approach for assigning function to DNA sequence-a pressing challenge in the age of high throughput sequencing technologies.

Scope of review: Here we review comparative genomic approaches that are bridging the sequence-function and genotype-phenotype gaps. Reverse genomic approaches aim to analyse sequence to assign function, whereas forward genomic approaches start from a phenotype and aim to identify the underlying genotype responsible.

Major conclusions: Comparative genomic approaches, pioneered in budding yeasts, have resulted in dramatic improvements in our understanding of the function of both genes and regulatory sequences. Analogous studies in other systems, including humans, demonstrate the ubiquity of comparative genomic approaches. Recently, forward genomic approaches, exploiting natural variation within yeast populations, have started to offer powerful insights into how genotype influences phenotype and even the ability to predict phenotypes.

General significance: Comparative genomic experiments are defining the fundamental rules that govern complex traits in natural populations from yeast to humans. This article is part of a Special Issue entitled Systems Biology of Microorganisms.

Fig. 1

The makeup of a complex trait. (a) Complex traits are regulated at the genetic level by multiple quantitative trait loci (QTLs), the environment and interactions between them (Adapted from Fig. 1 in reference 88). (b) Telomere length, as an example of a complex trait, consists of the number of repeats maintained at the end of the chromosomes. This is regulated by genes that modulate the activity of telomerase (e.g. YKU80) and genes whose activity is telomerase-independent (e.g. ELG1). Telomere length is also determined by environmental factors (including inhibitors of telomerase [85]) although this is yet to be comprehensively screened. Finally, interactions between genes (e.g. YKU70 and YKU80[83]) and between genes and the environment contribute to telomere length homeostasis.

Fig. 2

Different routes from genotype to phenotype. Complementary forward and reverse genetic approaches to understanding cellular traits.

Fig. 3

The phylogenetic footprint at a budding yeast replication origin identifies the functional protein-binding motif. Whole genome alignments from sensu stricto species can be analysed to identify phylogentically conserved motifs. Shown, is a region from an alignment spanning the replication origin ARS432.5. This identifies a conserved sequence element that matches the motif (called the ACS) found at S. cerevisiae replication origins. Mutation of this conserved motif was found to abolish origin activity . A second origin element (called the B1) is also found to be phylogenetically conserved . Bases conserved across all strains and species are shown in bold and highlighted in yellow, bases that differ from the European S. cerevisiae sequence are shown in blue. The alignment includes the five clean lineages of S. cerevisiae (European: DBVPG6765; West African: DBVPG6044; Malaysian: UWOPS03.461.4, Sake: Y12; and North American: YPS128), three clean lineages of S. paradoxus (European: CBS432; Far Eastern: N-44; American: YPS138), S. mikatae, S kudriavzevii, S. arboricolus and S. bayanus. *The sequence of ARS432.5 in the European S. cerevisiae strain is the same as the reference genome (S288c). ^§CBS432 is the S. paradoxus reference strain. Note the phylogenetic tree represents the topology of the sensu stricto group, but branch lengths are not drawn to scale.