Model organisms up close

Scientists are revealing the deepest annotations of the genomes of two of the most widely used model organisms in biology: __Caenorhabditis elegans__ and __Drosophila melanogaster__.

Caenorhabditis elegans
Image: Wikimedia commons

The findings appear this week in linkurl:two;http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09725.html linkurl:papers;http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09715.html in Nature and linkurl:one;http://www.sciencemag.org/content/early/2010/12/21/science.1196914 in Science. Launched in 2007 by the National Human Genome Research Institute, modENCODE aims to identify and map out all the functional elements of the __C. elegans__ and __D. melanogaster__ genomes. That includes the entire chromatin landscape as well as all the RNA transcripts, transcription factors, small RNAs, and origins of replications. Its complementary program, linkurl:ENCODE,;http://www.the-scientist.com/news/display/53280/ aims to do the same with the human genome.In a statistical and experimental tour de force, the modENCODE Consortium pulled together more than 700 gene expression data sets for __D. melanogaster__ and 237 for __Caenorhabditis elegans__ across several developmental stages."It's amazingly extensive work," said linkurl:David Fitch,;http://biology.as.nyu.edu/object/DavidFitch a geneticist at New York University who studies C. elegans morphogenesis but who did not take part in this effort. "Before, we had a road map of the [C. elegans] genome. Now we have a GoogleMaps map of the genome!"Among the new data presented are more than a thousand new genes for each organism (potentially completing their entire gene catalogues) as well as likely targets for all the transcription factors that were identified.

Drosophila melanogaster, male (left) and female
Image: Wikimedia commons

Of particular interest in the __Drosophila__ studies published by __Nature__, said linkurl:Peter Harte,;http://genetics.case.edu/?page_id=5&LN=Harte&FN=Peter a geneticist at Case Western Reserve University, is the identification of various "combinatorial chromatin states," each of which display different combinations of posttranslational modifications of histones together with binding of non-histone proteins with DNA."This work distinguishes a number of subclasses of active genes," characterized by different chromatin signatures, essentially moving away from a "one-size-fits-all" view of transcription, Harte said. One of the Nature linkurl:papers;http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09725.html also supports a more complex role for classic gene silencers such as the Polycomb group proteins. Binding of Polycomb near promoters is often associated with transcriptional silencing and trimethylation of Histone H3 on lysine 27 (a repressive modification), Harte explained. But the new data reveals that some Polycomb-bound genes are actively being transcribed, and this seems to depend on whether non-histone proteins, such as ASH1, are also present. "We're beginning to see that there are a variety of distinct classes of active and repressed transcriptional states that are each marked by unique chromatin signatures," Harte added.Not only do researchers hope that these detailed maps provide reference points for the human genome studies, but as evolutionary biologist from the University of Edinburgh, linkurl:Mark Blaxter,;http://www.nematodes.org/ wrote in the accompanying Science editorial, they will in time "deliver the power to model and predict organism function from multidimensional data."B.R. Graveley et al., "The developmental transcriptome of Drosophila melanogaster," Nature, doi:10.1038/nature09715, 2010.P.V. Kharchenko et al., "Comprehensive analysis of the chromatin landscape in Drosophila melanogaster," Nature, doi:10.1038/nature09725, 2010.M.B. Gerstein et al., "Integrative analysis of the Caenorhabditis elegans genome by the modENCODE Project," Science, 330: 1775-87, 2010.
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[19th March 2010]*linkurl:First pages of regulation;http://www.the-scientist.com/news/display/53280/
[13th June 2007]*linkurl:Post-genome project launches;http://www.the-scientist.com/news/20030305/02/
[5th March 2003]