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This Week in Genome Biology: Feb 20, 2019

Italian researchers propose a post-transcriptional modification-based stratification scheme for the brain cancer glioblastoma (GBM). Using RNA sequencing, the team tracked adenosine-to-inosine, or A-to-I, RNA editing in 145 de novo GBM tumors, 132 normal brain tissue samples, and a dozen pooled primary astrocyte brain cell samples. In addition to uncovering apparent high- and low-risk 'inosinome'-based GBM clusters, the analysis suggested that more than 85 percent of GBM tumors had deletions affecting a locus for ADAR3 — a brain-expressed gene suspected of regulating ADAR enzymes behind in post-transcriptional A-to-I RNA editing. "We propose that RNA editing at specific recoding sites may act as a 'driver' for tumor growth," the authors write, "and that GBM inosinome can be considered for a novel patient stratification method providing a systematic molecular understanding of sex differences in GBM."

A Peking University-led team takes a look at A-to-I RNA editing events in primates, comparing patterns in humans and rhesus macaques. For that analysis, the researchers used whole-genome sequencing and ribosomal RNA-depleted RNA sequencing, in combination with an analytical pipeline designed to pick up RNA edits, to search for such edits in rhesus macaque prefrontal cortex, cerebellum, heart, kidney, muscle, and testis samples, focusing in on more than 2.8 million potential RNA editing sites, most found at Alu repeat element sites. When they assessed ancestral and recent RNA editing sites with the help of additional data from half a dozen healthy humans and dozens more macaques, the investigators saw hints that relatively new RNA editing sites are over-represented in parts of the genome prone to guanine-to-adenine mutations.

Finally, researchers from the European Bioinformatics Institute and other sites in the UK and Germany present a single-cell analysis of gene expression and methylation in human induced pluripotent stem cells during the process of tissue differentiation. The team did single-cell RNA sequencing and single-cell bisulfite sequencing in parallel in nearly 200 individual cells. In the 84 induced pluripotent stem cells and 57 endoderm-bound cells that passed their quality control steps, the authors got a look at splice variants in the context of sequence composition, conservation, and DNA methylation profiles. "A combined model that is built based on genomic features as well as DNA methylation information accurately predicts different splicing modes of individual cassette exons," they write, including "conventional inclusion and exclusion patterns, but also more subtle modes of cell-to-cell variation in splicing."