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Stanford Researchers Put Nearly Complete Nematode Genome on a Chip

NEW YORK, Dec 26 - Researchers at Stanford University Medical Center said Tuesday that they have constructed DNA arrays containing 94% of the genome of the nematode Caenorhabditis elegans .

The researchers used the microarrays to profile gene expression during development and in the two sexes of C. elegans and found a total of 2,171 sex-regulated genes. This is a significant increase over the “handful” of previously known targets, according to lead researcher Stuart Kim.

C. elegans , a widely studied model organism whose full genome was sequenced in 1998, is the first organism to have such a large percentage of its genome included on a chip. The Stanford microarrays contain 17,871 out of the 18,967 genes currently annotated in the C. elegans genome. The full details of the project will be published in the January 2 issue of the Proceedings of the National Academy of Sciences .

Such large-scale DNA microarrays containing complete genomes will be necessary to study gene expression patterns, the next step toward understanding gene function using genome sequence data.

“Pre-genome, you would think 'what protein does [the gene] encode?' and then 'what happens if you knock out the gene?'” said Kim. “Post-genome, you’re going to have some massive amount of expression data about how that gene is regulated... No matter what gene you work on, there’s an expression dictionary that can be used to illuminate how these genes are working.”

The lab will make the DNA microarrays available to other C. elegans labs. RNA will be prepared in each of the individual labs, microarray experiments will be performed at Stanford and results will be reported over the web on the Stanford lab’s Worm Chip Directory database ( http://cmgm.stanford.edu/~kimlab/wmdirectorybig.html ).

The Stanford project is the second to include a nearly complete C. elegans genome on a chip, closely following the Genetics Institute and Harvard University, who published their paper in October in Science .

Kim’s lab is supported by academic research grants from the National Center for Research Resources, Merck Genome Research Institute, and Rhone-Poulenc Rorer/Gencell. Kim said the companies have no commercial claim on the microarrays.

 

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