Eddy, S.F. and Storey, K.B. 2008. Comparative molecular physiological genomics:
heterologous probing of cDNA
arrays. In: Environmental Genomics (Martin, C.C., ed.). Methods
in Molecular Biology, Volume 410, pp. 81-110. Humana Press,
Comparative Molecular Physiological Genomics: Heterologous Probing of cDNA Arrays
Sean
F. Eddy and Kenneth B. Storey
Abstract
The
use of DNA microarrays has gained wider acceptance as a standard tool for molecular
biology studies over the past decade. In particular, biomedical studies
embraced this technology as soon as arrays were produced for the common
laboratory species. Slower to develop, however, has been the use of microarray
screening with non-standard animal models, even though these species present
fascinating physiological phenomena for study. The very high cost and huge
amount of work involved in developing and producing a DNA array or microarray
for a new species is prohibitive for most researchers working in comparative
biology. The alternative is to explore the use of heterologous
array hybridization, screening for stress-induced gene expression in one
species using an array developed for another species. This chapter provides a
comprehensive review of the current literature on heterologous
DNA array hybridization and explores the factors that must be taken into
account when performing heterologous microarray
analysis on nonstandard species. Changes in methodology (e.g.
hybridization conditions, stringency of washing) to optimize the percent cross
reaction, the potential for false positives and false negatives to occur, and
techniques for downstream analysis and confirmation of array data are all
discussed. Examples of cross-hybridization using human microarrays are discussed
using phylogenetically diverse species ranging from
ground squirrels to frogs to snails. As with any new technology, the
willingness to grasp cross-species analysis has been slow but the future looks
bright for heterologous DNA hybridization and
microarray analysis now that the initial hurdles have been overcome.