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This Week in Genome Research: Jul 19, 2017

Investigators from the UK and Norway present findings from a population dynamics study of invasive Escherichia coli infections in England. Using whole-genome sequencing, the team assessed more than 1,500 E. coli isolates collected at hospitals in the UK over 11 years or from local E. coli sets from a diagnostic lab. These sequences made it possible to put together a pan-genome for the bug, along with a phylogenetic tree that pointed to the most prevalent E. coli lineages over time. Overall, the authors say, "these findings suggest that the frequency of E. coli lineages in invasive disease is driven by negative frequency-dependent selection occurring outside of the hospital, most probably in the commensal niche, and that drug resistance is not a primary determinant of success in this niche."

A Chinese Academy of Sciences- and University of Science and Technology of China-led team takes a look at long, non-coding RNAs (lncRNAs) in the rhesus macaque brain during development and aging. The researchers narrowed in on 18 lncRNA modules with RNA sequencing on eight brain regions in 1-, 4-, 10-, and 20-year-old rhesus macaques, followed by CAGE-seq to clarify transcription start sites, identifying lncRNA expression shifts associated with age, sex, and/or brain region. "Our findings offer a fresh insight into spatial-, age-, and sex-biased changes in lncRNA expression in the macaque brain," they say, "and suggest that the changes represent a previously unappreciated regulatory system that potentially contributes to brain development and aging."

Researchers from the US, UK, and China outline a scheme for doing targeted DNA mutation detection, RNA mutation detection, and gene expression profiling on single cells to tease apart tumor subclones, heterogeneity, and phylogeny. By applying this flow sorting-assisted approach to thousands of individual cells from five chronic lymphocytic leukemia (CLL) samples that had already been assessed by exome sequencing, the team identified apparent driver mutations in LCP1 and WNK1, genes not implicated in this process previously. "Integrative analysis to correlate genotype and phenotype revealed phenotypic convergence between distinct subclones," the authors report, "and unexpectedly found drivers of CLL not evident through analysis of bulk samples."