DNA Array Transcriptome Analysis

Brief Description:

 

Genome sequencing projects have let to the discovery of many gene sequences but not their function. Microarray technology can be used for large scale genotyping, gene expression profiling, comparative genomic hybrdization and resequencing among other applications. A DNA array is a collection of DNA spots, commonly representing single genes arrayed on a solid surface (glass, plastic, silicon chip or nylon). A solid phase assay has molecules attached to a solid support and these molecules are designated "capture molecules" or "probes". The capture molecules probe the sample for the presence of target molecules. The probe should have a high specificity and affinity for the target molecule as possible. The probes can be PCR products, oligonucleotides, or plasmids for the analysis of genomes and transcriptomes. The sample/target is allowed to react with the probes to generate probe-target interactions – also referred to as hybridization. After hybridization, target molecules are labeled using fluorescent molecules so that the probe-target hybridizations can be detected by generation of a signal. This technique gives the ability to test the interactions between thousands of genes simultaneously, when compared to traditional methods (Dufva 2009).

Whole-genome expression profiling can measure the transcriptional gene response to conditions or treatments of interest in a single assay, such as chemical or environmental agents (König et al. 2009). DNA microarrays have been used in gene expression profiling to give information about the relative differences in gene expression between two different cell populations. The transcriptome, the entire RNA complement of the cell, is dynamic – as opposed to the genome, which is generally regarded as static. The RNA population is dependent on genes being switched on and off in response to the prevailing environment. DNA arrays are now used to determine the location of transcription factor binding sites, to identify protein-RNA interactions, and to detect differences in both DNA content or sequence between yeast strains by comparative genome hybridization.

Application in Wine Microbiology:

DNA microarrays have been most widely used in wine research. These studies include gene expression during fermentation and during exposure to a variety of stresses such as sub-lethal ethanol concentrations, rehydration, and high sugar stress. Variation present across wine yeast strains has been investigated to correlate winemaking performance of individual strains to particular genomic attributes. In 2007, there were over 200 microarray datasets concerning Saccharomyces cerevisiae in the Gene Expression Omnibus public microarray database.

An area of great potential to the wine industry is the use of high resolution comparative genome hybridization for the mapping of complex trait loci or interstrain polymorphisms. This will potentially enable rapid identification of loci that are responsible for imparting positive attributes from existing wine yeast strains. Once identified, these desirable loci could be specifically assembled into single strains using classical approaches to maximize strain quality (Borneman et al. 2007). The utilization of DNA microarrays will enable winemakers to strategically select yeast strains to specifically tailored wines for a given consumer base, despite seasonal variation in grape composition or changes in consumer preferences, resulting in maximum profits for wineries.

References:

  • Borneman, A. R., P. J. Chambers, I. S. Pretorius. 2007. Yeast systems biology: modeling the winemaker's art. Trends Biotechnol. 25:349-355.
  • Dufa, M. (ed.). 2009. DNA Microarrays for Biomedical Research: Methods and Protocols. 529:1-22.
  • König, H. et al. (eds.). 2009. Biology of Microorganisms on Grapes, in Must and in Wine. Springer-Verlag Berlin Heidelberg.