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This Week in PNAS: Nov 8, 2016

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from Spain, Germany, Japan, and Brazil describe a long non-coding RNA that assists in TP53 tumor suppressor activity, but is inactivated by hypermethylation in some cancer. The team did array-based methylation profiling in colon cancer cell lines with or without disrupted methyltransferase enzymes, along with normal colon mucosa. Based on methylation patterns at hundreds of thousands of cytosine bases, including sites in 104 lncRNAs, the group uncovered enhanced methylation in the promoter of TP53TG1 — a lncRNA that binds YBX1 and contributes to TP53-mediated DNA damage response. From these and other experiments, the authors conclude that "TP53TG1 epigenetic inactivation in cancer cells releases the transcriptional repression of YBX1-targeted growth-promoting genes and creates a chemoresistant tumor."

A team from US and Costa Rica explores the production of an antifungal compound called selvamicin, made by Pseudonocardia bacteria living in fungus-growing Apterostigma ants. Using genome sequencing and other approaches, the researchers compared selvamicin biosynthesis by Pseudonocardia isolates from ants in neighboring colonies at sites in Costa Rica. The same cluster of selvamicin biosynthesis genes turned up in microbes from both ant colonies, they report, though one of these was located on a plasmid and the other was embedded in a bacterial chromosome. "These alternative genomic contexts illustrate the biosynthetic gene cluster mobility that underlies the diversity and distribution of chemical defenses by the specialized bacteria in this multi-lateral symbiosis," the group writes.

The Max Planck Institute for Developmental Biology's Detlef Weigel and colleagues report on the genetic architecture they detected in Arabidopsis thaliana hybrids formed by crossing 30 sequenced parental plant accessions. With the help of genome-wide association mapping methods, the team focused on non-additive genetic inheritance patterns in 435 first-generation hybrid Arabidopsis representatives stemming from such crosses, uncovering sites in the genome that seem to contribute to processes such as hybrid vigor.