In PLoS Biology this week, investigators in Belgium present cisTargetX, a new computational method "that predicts transcription factor binding motifs and their target genes through the integration of gene expression data and comparative genomics." Using three Drosophila species, the team first validated their method in silico; their subsequent perturbations of predicted neurogenesis transcription factors and gene-expression analyses via microarrays, showed the team that "cisTargetX efficiently predicts genetic regulatory interactions and provides mechanistic insight into gene regulatory networks of postembryonic developmental systems."
Also in PLoS Biology, researchers at the University of Münster Institute for Experimental Pathology "provide evidence from newly established and virtually homoplasy-free retroposon insertion markers for the basal relationships among marsupial orders." Specifically, the team screened 217,000 retroposon-containing loci from opossum and kangaroo in silico and deduced 53 phylogenetically informative markers. The authors say that their study "provides important insight into the evolution of retroposable elements in the marsupial genome," and that, when combined with paleobiogeographic information, this retrotransposon insertion pattern "indicates a single marsupial migration from South America to Australia." In an accompanying editorial, Mason Inman says that "jumping genetic elements are themselves shifty, but they could help settle the science."
Over in PLoS Genetics, an international research team led by investigators at North Carolina State University reports their "quantitative and molecular genetic analyses of mutations increasing Drosophila life span." They confirmed 58 mutations for increased longevity in the fruit fly, the effects of which they also confirmed to be highly sex-specific. "Mutations in the same gene were associated with both increased and decreased life span, depending on the location and orientation of the P–element insertion, and genetic background," the authors write, adding that a "comparison of transcript profiles of long-lived mutations and the control line reveals a transcriptional signature of increased life span."
Investigators at the University of Maryland and their colleagues this week report that three genes — hrg-4, mrp-5, and F22B5.4 — are "vital for organismal heme homeostasis in C. elegans." With gene-expression array and RNAi-mediated knockdown experiments, found a "catalog of genes that are essential for metazoan heme homeostasis" in the nematode, some of which, they write, have putative homologs in humans. They conclude that their work demonstrates "the power of C. elegans as a genetic animal model to dissect the regulatory circuits which mediate heme trafficking in both vertebrate hosts and their parasites, which depend on environmental heme for survival."