a Whole Genome Array Approach - Jacobs University

Background
1.4 Gene expression profiling by DNA microarray analysis
The genome annotation of R. baltica combined with the experimental work that has been
carried out on this organism and on other members of the Planctomycetes provided new
information and generated hypotheses about the metabolic capabilities and life-style of these
organisms. However, in order to turn these mostly computationally derived hypotheses into
real biological knowledge there is an urgent need to verify the predicted gene functions by
experiments using different molecular techniques, for example gene expression profiling.
Gene expression is a highly complex and tightly regulated process that allows a cell to
respond dynamically both to environmental stimuli and to its own changing needs. This
mechanism acts as both an “on/off” switch to control which genes are expressed in a cell, and
as a ”volume control” that increases or decreases the level of expression of particular genes as
necessary (Dupont et al. 2007). Gene expression analysis examines the composition of
cellular messenger RNA populations.
Traditional gene expression analysis has used techniques such as Northern blotting, RT-PCR
and nuclease protection assays. More advanced methods – some of these include differential
display, subtractive hybridisation, representational difference analysis, expressed sequence
tags, cDNA fragment fingerprinting, and serial analysis of gene expression – have enabled the
discovery of novel differentially expressed genes. However, the technical challenges of these
methods still limit their use to the analysis of just a few samples/genes at a time. Microarray
analysis, in contrast, allows the analysis of thousands of genes in multiple samples with
relative ease (Duggan et al. 1999).
Gene expression analysis using DNA microarrays has been applied to numerous mammalian
tissues, yeast (Alizadeh and Staudt 2000), and bacteria alike (Hu et al. 2005; Steglich et al.
2006). These studies examined the effects of different chemicals on cells, the consequences of
over-expression of regulatory factors in transfected cells, and compared mutant strains with
parental strains to delineate functional pathways. In cancer research, microarrays have been
used to find gene expression changes in transformed cells and metastases, to identify
diagnostic markers, and to classify tumours based on their gene expression profile (Amersham
2002). Lately, transcriptional profiling is even applied to study environmental questions
(Zhou 2003; Parro et al. 2007). Dupont and co-workers expect this to be the major activity of
ecological genomics in the near future (Dupont et al. 2007).
10