Friday, December 16, 2005

The Competitive World of Gene Naming

Many genes have names, most do not. Drosophila geneticists are among the most clever at naming genes. Historically, genes have been named by the phenotype of the first mutation in that gene. For example, the first Drosophila mutation discovered disrupted a pigmentation pathway and cause the fly's eyes to be white (as opposed to the wild-type red hue). Thomas Hunt Morgan's lab named this mutation white, and now the gene is also known as white.

The white gene is a particular bad example of clever naming, but it does illustrate the naming process. Some of the more fun names include fruitless (that I've blogged on before and used to be known as fruity), tinman (problems with heart development), and Scott of the Antarctic (which makes me think of this). Other research communities have different ways of naming genes. Yeast geneticists are among the least interesting (when it comes to naming genes), using a combination of three letters and a number. The mouse/rat community seems to have dry naming rules as well, but it's hard to tell. One of my all time favorite gene names pays homage to the second greatest video game character of all time (behind Mario, of course), Sonic the Hedgehog. Mutations in the Drosophila gene hedgehog (which affects segmentation patterning) causes the embryo to look like a balled up hedgehog. When the homologous gene was identified in zebrafish in 1993, it was named sonic hedgehog after the popular video game.

Whole genome sequencing has added an extra dimension to the naming game. One of the first steps after assembling a completed genome is the annotation. This requires identifying all of the protein coding genes, tRNAs, rRNAs, transposable elements, and any other class of sequences in the genome using gene finding algorithms and alignments with closely related known sequences (including other sequenced genomes). The annotation process, however, is drastically different than traditional gene naming. During annotation, genes are assigned unique identifiers (usually some sequence of letters and numbers) regardless if the gene was named using a classic mutation experiment. Genes that were never named via mutagenesis (or some other molecular analysis of function) only go by their boring annotation identifier, but previously characterized genes get to keep their old names as well.

That brings me to a sad piece of news reported in Nature:
"A cancer research institute has been threatened with legal action by the US branch of Japanese video-game franchise Pokemon, after one of its researchers borrowed the company's trademark to name an oncogene."
The authors of the paper in question use the name Pokemon as a clever abbreviation for the genes functional description, POK erythroid myeloid ontogenic. Around the time of publication the paper received a fair bit of press, and people began saying things like, "Pokemon causes cancer." Not surprisingly, that got the folks behind the TV-show/video-game in a tizzy. Pokemon may cause seizures (the TV show not the gene), but the show does not cause cancer (although aberrant expression of the gene is found in cancer cells).


At 12:06 AM, Blogger pluripotentate said...

clever or dry, naming homologous genes something utterly different from species to species is holding science back pretty badly, i think. say a mouse protein is called abcd. those researchers certainly don't know to search the literature for its homologue "flashy" when they go looking to see if the zebrafish folks know something they don't.


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