Worm Breeder's Gazette 15(3): 10 (June 1, 1998)

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

Using cDNA microarrays for Differential Gene Expression Studies

John Wang, Carrie B. Van Doren, Stuart K. Kim

Dept. of Developmental Biology, Stanford U., Stanford, CA 94305.

        We are currently adapting a cDNA microarray-based method for
monitoring differential gene expression for use in worms. DNA
microarrays consist of PCR fragments that have been robotically
deposited onto treated microscope slides.  To analyze differential gene
expression between two strains, cDNA probes are made from each strain
using fluorescently-labeled nucleotides.  Two probes, each labeled with
a different fluorescent dye, are simultaneously hybridized to a
microarray.  The microarray is scanned with a scanning confocal-laser
microscope and the emission intensity of each fluorescent dye at every
location on the array is measured.  By normalizing to total
hybridization signals from each probe, relative differences in
hybridization intensity can be determined, permitting us to calculate
gene expression differences.  For example, cDNA probe prepared from
wild-type and a mutant might be labeled green and red, respectively. 
Green spots would represent genes that are expressed less in the mutant
relative to wild-type.  Conversely, red spots would represent genes that
are more highly expressed in the mutant relative to wild-type. Genes
expressed at similar levels would appear yellow.
        One powerful application of the microarray is to identify
transcriptional differences in a mutant versus wild-type.  In
particular, genes that act redundantly with other genes could be
identified.  A limitation of the microarray-based approach for worms is
that isolation of RNA must occur from whole worms.  Thus, the microarray
may not be sensitive enough to detect differences in transcripts that
are only present in a few cells.  Alternatively, constitutive gene
expression in tissues outside of the cells of interest may obscure
relevant gene expression differences.
        Currently, we have produced a 1264 element array, of which 1152
elements are PCR products from a library of random C. elegans ESTs
(generously provided by Yuji Kohara at National Institute of Genetics,
Japan). In collaboration with Jeremy Nance and Sam Ward, we have used
the DNA microarrays to identify potential sperm and oocyte enriched
genes.  As described in an accompanying Gazette article, the sperm
enriched genes identified in this experiment included a number of major
sperm protein genes, and the oocyte enriched genes identified several
meiosis and maternally expressed genes.  We have begun to identify genes
regulated by the MAP kinase signaling pathway in vulval development.
        We welcome collaborations with any persons interested in
applying microarray technology to their studies.