Pseudogenes get some respect

Pseudogenes are the non-functional remnants of genes that have been thought to do nothing more than take up space. A new report by Shinji Hirotsune and colleagues provides evidence that at least one such pseudogene has an essential role as a regulator of gene expression (Nature 423, 91–96; 2003). A fortuitous insertion of a transgene into the Makorin1-p1 locus generated a mouse with a bone deformity and polycystic kidneys. Makorin1-p1 is a pseudogene that is normally transcribed, although no functional protein product can be produced. Strikingly, the transgene insertion reduced not only the transcription of Makorin1-p1, but that of its functional homolog, Makorin1, as well. In vitro experiments show that an intact Makorin1-p1 locus stabilizes the Makorin1 mRNA, and a rescue of the original transgenic mouse with Makorin1-p1 proves that the pseudogene is required for normal expression of Makorin1. The authors postulate that Makorin1-p1 may titrate out a factor that destabilizes the Makorin1 transcript, thereby increasing Makorin1 expression in a developmentally regulated manner. With about 20,000 pseudogenes in the human genome, further examples of this kind no doubt await discovery. AP

Flyin' pain free

Nociception, the sensing of painful stimuli, has been studied in mammals for decades, but there has not been a robust model system to study the genetics of pain. W. Daniel Tracey, Jr. and colleagues have now described an assay in Drosophila larvae for the detection of pain (Cell 113, 261–273; 2003). They show that in response to a hot probe or mechanical pinching of the cutical, wild-type larvae roll in a characteristic sideways corkscrew motion. A forward genetic screen of 1,500 previously isolated P-element lines resulted in the isolation of the first Drosophila mutant for pain sensation, appropriately named painless. The painless gene encodes a new member of the transient receptor potential ion channel family, which had been previously implicated in nociception and mechanosensory transduction. Suction electrode recordings of sectioned abdominal nerves showed that spike frequencies in painless mutants did not change dramatically as the temperature was raised to 42 °C, as opposed to wild-type embryos, whose firing rate nearly doubled. Characterization of the 48 additional nociception-defective lines identified in the screen will certainly add new dimensions to our understanding of pain. MS

Can a virus outsmart glioma?

Glioma is a lethal brain cancer that can resist radiation and chemotherapy. Adenovirus-based treatment has been difficult, but a new viral system has now shown unprecedented success. Juan Fueyo and colleagues genetically manipulated an adenovirus to effectively destroy a tumor from the inside out (J. Natl. Cancer Inst. 95, 652–660; 2003). First, they developed a tumor-selective adenovirus, Delta-24, with a deletion in E1A that disrupts its ability to bind retinoblastoma (Rb) protein. In normal cells, Rb prevents viruses from entering, so Delta-24 can replicate only when Rb is inactivated, as in cancer cells. Delta-24 killed the tumors but had low infectivity, possibly owing to the low concentration of coxsackie-adenovirus receptors on the surface of cancer cells. Because adenoviral entry is mediated by interaction between RGD motifs and integrins, they went on to engineer a virus with an RGD peptide. This version of the modified virus specifically infected tumor cells and replicated more effectively than Delta-24. When injected directly into human gliomas xenografted into mice, Delta-24-RGD allowed significantly longer survival than did Delta-24 or an inactivated virus control. More impressively, 60% of mice treated with Delta-24-RGD were long-term survivors (compared with 15% of those treated with Delta-24 characterized by complete tumor regression). MH

RNAi on or off target?

Two new reports examine the specificity of RNA interference (RNAi) in human cells using genome-wide expression profiling. Targeting exogenous GFP in human embryonic kidney cells, Jen-Tsan Chi and colleagues report efficient and specific knockdown using two different siRNAs (Proc. Natl. Acad. Sci USA 10.1073/pnas.1037853100). Analysis of approximately 20,000 genes identified no consistent gene expression profile and no statistically significant difference in global gene expression patterns associated with the two siRNAs. Further analyses did not identify spreading of the RNAi effect to similar exogenous sequences, leading the authors to conclude that the RNAi effect is on target in mammalian cells. In a related paper, Peter Linsley and colleagues targeted endogenous genes (Nat. Biotechnol. 10.1038/nbt831). They examined the effect of 16 different siRNAs against IGF1R and 8 different siRNAs targeted against MAPK14. In each case, the gene expression profile was siRNA-specific. A group of 9 genes with partial sequence identity to the siRNA duplex targeted against MAPK14 were downregulated with similar kinetics. The authors conclude that at least some cross-hybridization of siRNAs to transcripts of similar sequences occurs. These results suggest that ensuring siRNA-specific effects requires well controlled experiments. DG

History to the rescue

The analysis of sequence variation on the Y chromosome provides a powerful tool for studying a population's genetic ancestry. Matthew Hurles and colleagues have now used it to uncover the genetic impact of a historical episode during the Polynesian slave trade (Am. J. Hum. Genet. 72, 1282–1287; 2003). Genetic evidence suggests that Polynesians originally came from South East Asia. But an earlier study by the authors indicated that inhabitants of one Polynesian island, called Rapa, had Y-chromosomal markers specific for Native Americans. A closer look at Rapan Y chromosomes and mitochondrial DNA shows that this population, unlike those of other Polynesian islands, contains substantial levels of European and Native American admixture. To explain this, Hurles et al. hit the history books. The Peruvian slave trade caused depopulation of many Polynesian islands from 1862 to 1863. In 1863, Rapans captured the Peruvian slave ship Cora. Most members of the crew were sailed to Tahiti for trial, but five remained on Rapa. These five men were probably of Native American origin, possibly with European admixture. If these men had children, we could expect to see their genetic contributions in the Rapan population, especially because shortly after their arrival on the island, Rapans were devastated by an epidemic of dysentery or smallpox, to which the marooned sailors may have been more resistant. LB

Research Notes written by Laura Bonetta, David Gresham, Monica Harrington, Alan Packer and Michael Stebbins.