From Gene to Whole Genome

Thirty years ago the Southern blot hybridization revolutionized gene analysis, allowing single genes to be studied within complex genomes [7]. Soon techniques such as reverse-transcription polymerase chain reaction (RT-PCR) and versions of the Northern blot followed. These allowed quantification as well as detection of RNA molecules but remained limited to single genes. This limitation was reduced with the development of macroarrays using nylon membranes to support many genes at once. However, the introduction of the microarray made it possible to study the expression of every single gene within a genome at once [8, 9]. The first technological advance that was key to the development of the microarray was the use of glass as a solid substrate for the DNA probes. This allowed many more probes to be accurately held on one surface and in a much smaller area. The second was the development of printing methods that increased the resolution and accuracy of printing onto a glass surface.

The genome-wide study of the complete (whole organism) mRNA expression profile (the transcriptome) is known as transcriptomics. Although transcriptomics -the comparison of a control and an experimental sample's expression profile - is the primary application for microarrays, they can be used for many purposes including the analysis of genome structure and as a strain-screening tool. The conclusions being drawn from pathogen microarray studies are revolutionizing microbiology. Our understanding of microbial pathogenesis is adapting to the view that bacterial activities are the product of a whole organic system rather than the activity of a single gene or regulon. Host responses to microbial infection are also being characterized using host genome microarrays. Studying both the bacterial and host expression profiles during infection will provide the most complete understanding of host-pathogen interactions.

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