In this week's Nature Ecology & Evolution, a team led by researchers from the University of Potsdam publishes a study identifying a genomic link between ancient cave bears —which went extinct about 25,000 years ago — and modern-day brown bears. The scientists sequenced nuclear genomic DNA from bone samples of four cave bears, which they analyzed against the sequenced genomes of several ancient and modern brown bears, as well as other types of bears. They find that cave bear DNA persists in the genomes of living brown bears, accounting for 0.9 percent to 2.4 percent of the genomes of all brown bears studied — findings that point to interbreeding between the two species. The results demonstrate that although extinction "typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species." GenomeWeb has more on the study, here.
And in Nature Communications, a group of Chinese and US investigators reports data showing that sodium benzoate incorporates into the epigenomes of cells in culture, suggesting that this common food preservative may have unexpected biological effects. The researchers used proteomic and biochemical techniques to identify a novel histone mark — called lysine benzoylation — in cultured cells, while ChIP-seq and RNA-seq analyses demonstrate that it could influence gene expression related to metabolic pathways such as insulin secretion. Additional study revealed that sodium benzoate can stimulate the generation and accumulation of this histone mark.
Meanwhile, in Nature Medicine, an international research team publishes genome-scale maps of DNA methylation in glioblastoma — a particularly deadly form of brain cancer — that reveal tumor heterogeneity in time and space. The scientists perform DNA methylation mapping in a large set of routinely collected formalin-fixed, paraffin-embedded tumor samples, and use bisulfite sequencing as a multipurpose assay to infer a range of different genetic, epigenetic, and transcriptional characteristics of the profiled tumor samples. Among their findings are differences between primary and recurring tumors, links between DNA methylation and the tumor microenvironment, and an association of epigenetic tumor heterogeneity with patient survival. The work represents "an open resource for dissecting DNA methylation heterogeneity in a genetically diverse and heterogeneous cancer," the authors state.