Functional Genomics in C. elegans 1:

Microarray Analysis of Gene Expression

(1: Microarray analysis 2: Expression analysis using reporters 3: RNAi)

With the sequenced genome available, and the extensive EST dataset from the Kohara laboratory it is now possible to contemplate research approaches that address the whole genome. One such approach is the use of arrays of expressed DNA segments as hybridisation targets to examine gene expression levels. There is an excellent description of the technology behind the experiments and analysis of microarray experiments at http://www.cs.washington.edu/homes/jbuhler/research/array/experiment.html

This collection of DNA fragments can be printed in dense arrays on glass slides, and the slide used for hybridisation assays.

Next, two (or more) probes are generated from mRNA from the two strains being compared. [Its also possible to compare stages, or differently treated nematodes (drug + vs drug-, for example)]. The probes are labeled using fluorescently tagged nucleotides. These are excited by a laser, and their fluorescence read by a tuned spectrophotometer (much as an autoomated sequencing gel is read).

For example, here is a set of data from an experiment examining differences between two different nematode strains. One was N2 wild type, the other was mutant in the let-60 gene. The let-60 gene encodes a Ras homologue involved in many cell fate determination decisions in the embryo, and also in processes in later development, such as vulva formation. The image is from the Kim lab web site.