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This Week in Nucleic Acids Research: Mar 15, 2017

Researchers from Thomas Jefferson University describe differential expression patterns for human microRNA isoforms that may help distinguish cancer types. The team tallied the presence or absence of so-called isoforms of human miRNA (isomiR) levels in nearly 10,300 tumors samples from the Cancer Genome Atlas Project, coming up with a cancer type classifier based on the almost 7,500 isomiRs identified. A whittled-down version of the classifier appeared to successfully distinguish between the 32 cancer types considered for TCGA, while correctly classifying between 76 percent and 100 percent of samples in seven more datasets.

A team from Texas A&M University and the University of Massachusetts outlines and assesses a computational strategy for teasing genetic interactions patterns out from transposon insertion sequencing (Tn-seq) data. The researchers applied the statistical method to profile genetic interactions for a handful of Mycobacterium tuberculosis genes with unknown functions, using TN-seq libraries and isogenic M. tuberculosis strains under selection in mice. "While the genes necessary for in vitro growth are common to other bacteria, and are comparatively well annotated, a large fraction of the genes specifically necessary for infection are specific to mycobacteria and have not been assigned to functional pathways," the authors note.

Finally, researchers in Canada and Argentina report on findings from an analysis of virulence gene expression in the brucellosis-causing intracellular pathogen Brucella, which focused on genes targeted by a LuxR-type transcription factor regulator called VjbR. Using a combination of chromatin immunoprecipitation sequencing and RNA sequencing, the team profiled sites in the Brucella genome that are bound to VjbR and looked at the ways that this regulator binding affected the pathogen's gene expression under conditions similar to those in an infected eukaryotic cell. The authors argue that the results "provide a comprehensive mapping of the VjbR binding across the genome of Brucella abortus and bring new insights into the VjbR-mediated mode of control of global gene expression of this intracellular pathogen."