Expression profiling by array Genome variation profiling by array
Summary
Whole genome sequencing, particularly in fungi, has progressed at a tremendous rate. More difficult, however, is experimental testing of the inferences about gene function that can be drawn from comparative sequence analysis alone. We present a genome-wide functional characterization of a sequenced but experimentally understudied budding yeast, Saccharomyces bayanus var uvarum (henceforth referred to as S. bayanus), allowing us to map changes over the 20 million years that separate this organism from S. cerevisiae. We first created a suite of genetic tools to facilitate work in S. bayanus. Next, we measured the gene expression response of S. bayanus to a diverse set of perturbations optimized using a computational approach to cover a diverse array of functionally relevant biological responses. The resulting dataset reveals that gene expression patterns are largely conserved, but significant changes may exist in regulatory networks such as carbohydrate utilization and meiosis. In addition to regulatory changes, our approach identified gene functions that have diverged. The functions of genes in core pathways are highly conserved, but we observed many changes in which genes are involved in osmotic stress, peroxisome biogenesis, and autophagy. A surprising number of genes specific to S. bayanus respond to oxidative stress, suggesting the organism may have evolved under different selection pressures than S. cerevisiae. This work expands the scope of genome-scale evolutionary studies from sequence-based analysis to rapid experimental characterization and could be adopted for functional mapping in any lineage of interest. Furthermore, our detailed characterization of S. bayanus provides a valuable resource for comparative functional genomics studies in yeast.
Overall design
Samples GSM1153177-GSM1153193 represent gene expression and transposon mapping arrays. The other arrays from the paper are also available from GEO accession GSE16544.
The arrays indicated as "alpha factor" are gene expression arrays. The mutant and wt strains, as indicated, were exposed to alpha factor and sampled for gene expression at the time indicated. Each sample was hybridized versus a common mixed reference, as described in the manuscript.
The Tn7 array uses Transposon Specific Extraction to map the location of an insertion element. The extracted sample is hybridized versus genomic DNA.
Less...
More...