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This Week in PLOS: Sep 17, 2012

A genome-wide association study appearing in PLOS Genetics that involved thousands of individuals of European ancestry identified five genetic loci that appear to be associated with facial features. Among them: variants in and around genes implicated in prior studies of conditions that are characterized by face and/or skull malformations. The researchers behind the study, members of the International Visible Trait Genetics, or VisiGen, Consortium, argue that the new findings could contribute to what's known about facial evolution and development in humans, while at once laying the foundation for forensic tools for predicting facial features based on DNA alone. For more on this study, see this story from our sister publication GenomeWeb Daily News.

Investigators from the Cleveland Clinic and elsewhere used post-mortem brain samples to look at the epigenetic and transcriptional profiles associated with autism spectrum disorder. As they reported in PLOS One, the researchers relied on arrays and bisulfite sequencing to assess genome-wide gene expression and DNA methylation profiles in two brain regions — the cerebellar hemisphere cortex and the Brodmann area 19 occipital cortex — in samples from nine males with idiopathic cases of autism spectrum disorder and nine unaffected male controls in the same age range. Overall brain expression patterns varied from one individual with ASD to the next. But the team did uncover some shared features within the ASD samples, including lower-than-usual expression of genes in mitochondrial oxidative phosphorylation and protein production pathways in the brain samples from individuals with autism and shifts in the expression of certain brain-related genes.

A PLOS Pathogens study of dengue virus by French researchers explores the basis for the pronounced conservation that's been noted in nucleotides found at the ends of the virus' RNA-based genome. Using chemical synthesis experiments, assays, and other analyses, the group determined that the virus, a representative of the Flavivirus genus, relies on an RNA end-repair process that involves the RNA-dependent RNA polymerase produced by a dengue virus gene called NS5. "Our findings provide a direct demonstration of the implication of a viral RNA polymerase in the conservation and repair of genome ends," the study's authors wrote. "Other polymerases from other RNA virus families are likely to employ similar mechanisms."

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.