Bioinformatics

Trait-to-gene: a computational method for predicting the function of uncharacterised genes. Levesque, M. et al. Curr. Biol. 13, 129–133 (2003)

This group have developed algorithms to infer gene function based on correlations between the presence of genes and a particular phenotype. The algorithms were tested in a search to find the genes involved in flagella development, and successfully identified genes already known to be involved in flagella function, as well as two uncharacterized genes that if inactivated (in Bacillus subtilis) result in impaired mobility.

Genomics

Release 3 of the Drosophila genome. Genome Biol. 3, research0079–0088 (2002)

The Berkeley Drosophila Genome Project, FlyBase and colleagues have produced this collection of 10 papers covering the completion of the Drosophila genome sequence and its annotation, along with a description of functional studies and computational tools. The new release of the genome sequence confirms the utility of the whole-genome shotgun strategy but also highlights flaws in the initial method of repeat assembly. Furthermore, it has some immediate practical benefits, allowing defective clones to be weeded out from the collection of full-length Drosophila cDNAs (the Drosophila Gene Collection). The bioinformatic strategies and software used to annotate the sequence are among the most sophisticated available, yet manual curation is still an essential step in the annotation process. Nonetheless, the sequencing and annotation strategies accurately defined the intron–exon structures of 30 known protein-coding genes and 267 protein-coding gene models in the notoriously difficult heterochromatic sequences. The new release also has the first characterization of transposable elements in the euchromatic genome sequence. Drosophila developmental genomics gets a boost with the embryonic expression patterns of 2,179 genes being examined in fixed Drosophila embryos. Comparative genomics and the computational identification of core promoters in the fly genome are also covered in this comprehensive collection that, having been available online, is now published in print.

Technology

A lentivirus-based system to silence genes in primary mammalian cells and transgenic mice by RNA interference. Rubinson, D. A. et al. Nature Genet. 18 February 2003 (10.1038/ng1117)

Although RNAi works efficiently in many organisms, including mammals, some cell types remain refractive to it, mainly because of transfection problems. Rubinson and colleagues show that lentiviral delivery of short hairpin RNAs overcomes this problem and leads to efficient functional gene silencing in vivo and in vitro in many cell types, including mitotic and post-mitotic cells, stem cells and zygotes. The authors suggest that, if used to silence disease-causing genes, this method might have a therapeutic potential.