Unlocking the secrets of the genome.

Department of Genome Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
Nature (Impact Factor: 41.46). 07/2009; 459(7249):927-30. DOI: 10.1038/459927a
Source: PubMed


Despite the successes of genomics, little is known about how genetic information produces complex organisms. A look at the crucial functional elements of fly and worm genomes could change that.

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    • "One observation supporting that most of them are in fact ncRNA genes is that their expression breadth is quite different from that of PCGs and a high fraction of them are stage-specific genes. In most Drosophila species, with limited analyses of the transcriptome (Celniker et al. 2009), few ncRNA genes have been annotated. By contrast, in D. melanogaster with a very well annotated genome, 2,096 ncRNA genes have been found (Release 5.56, FlyBase). "
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    • "Consistent with this hypothesis, we find that ectopic expression of AbdA also abrogates mitotic behavior in DT cells in Tr2 (Figures S4A and S4B). Mitotic activity triggered by overexpression or lowering of Ubx protein is associated with changes of fzr expression (Figures 4D, 4F, and 4H), and the Drosophila modENCODE has shown direct binding of Ubx protein to the fzr promoter (Celniker et al., 2009) providing a mechanistic link accounting for this shift between endocycling and mitotic activity. "
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    • "For example , the expression of gene families involved in insecticide metabolism is enriched in the midgut of Drosophila melanogaster (Li et al. 2008), and transgenic overexpression of various members of these gene families in the midgut, Malpighian tubules, and fat bodies confers resistance to insecticides (Chung et al. 2007; Daborn et al. 2007, 2012), and in honeybees, the products of at least two separate metabolic pathways were detected in the midgut after feeding them with radiolabeled imidacloprid, a neonicotinoid insecticide (Suchail et al. 2004). Gene expression in databases such as FlyAtlas and modENCODE is reported for intact midguts (Chintapalli et al. 2007; Celniker et al. 2009), but there are differences in gene expression, cell type, morphology , and lumen acidity in different subsections of the midgut. Based on the pH in the lumen, the midguts of insects can be separated into at least three compartments (Terra and Ferreira 1994). "
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