Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.
University of Lyon researchers describe transcriptional shifts affecting transposable elements (TE) in Drosophila fruit flies with viral infections in a paper scheduled to appear in PNAS this week. Past research has shown that both Piwi-interacting small interfering RNA (piRNA) and small interfering RNA (siRNA) pathways contribute to TE responses in insects, they note, with siRNAs playing additional roles in defense against viruses. That prompted the team to track transcriptomic and other consequences of Sindbis virus infections in Drosophila using RNA sequencing, small RNA sequencing, and other approaches. The experiments suggested "viral infections affect TE transcript amounts via modulations of the piRNA and siRNA repertoires, with the clearest effects in somatic tissues," the authors report. "These results suggest that viral acute or chronic infections may impact TE activity and, thus, the tempo of genetic diversification."
A team from the US and Canada examines gene expression patterns and broader transcriptomic networks at play in developing maize plant leaf cuticles over time and space using an approach called laser microdissection RNA sequencing (LM-RNAseq) in combination with weighted gene co-expression network analyses. "Plant cuticles are composed of wax and cutin and evolved in the land plants as a hydrophobic boundary that reduces water loss from the plant epidermis," the authors explain. "The expanding maize adult leaf displays a dynamic, proximodistal gradient of cuticle development, from the leaf base to the tip." When they assessed samples collected along this proximodistal gradient, the researchers saw an apparent role for the PHYTOCHROME light receptors in the wax depositing process of cuticle development in maize — a feature that appeared to be shared by Physcomitrella patens moss in subsequent reverse genetic analyses.
Researchers from the US, China, and the UK take a closer look at versions of the hypoxia inducible factor (HIF) pathway genes PHD2 and HIF2A that have been implicated in high-altitude and low-oxygen adaptations within the Tibetan population in past genome-wide association studies. Using in vitro protein interaction assays, mouse model experiments, and other approaches, the team characterized PHD2 alleles present in Tibet, demonstrating that multiple hypoxia-related mutations prompt loss-of-function changes in the gene, which forms a protein that degrades the HIF2A gene product. "We propose that Tibetans possess genetic alterations that both activate and inhibit selective outputs of the HIF pathway to facilitate successful adaptation to the chronic hypoxia of high altitude," the authors write.