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This Week in Genome Research: Feb 27, 2019

A Stanford University School of Medicine-led team has developed a CRISPR-based way to tease out genetic interactions, noting that yeast-based screens can be unwieldy. As they report in Genome Research, the researchers used a CRISPR interference approach to knock down single genes in yeast and combined it with sequencing to form a new tool dubbed CRISPRiSeq. They applied CRISPRiSeq to search for genetic interactions between about 7,700 gene pairs in five different experimental conditions using about 17,000 strains. This approach, they say, enabled them to uncover about three times as many interactions as in rich media alone.

A duo from the Harvard T.H. Chan School of Public Health and the Broad Institute reports that ribosomal DNA can be used to estimate individual ages within a species. They hypothesized that, as rDNA has been linked to aging, its methylation could serve as marker of aging, a notion they tested in mice, canids, and humans. They found that their CpG methylation-based clock could predict chronological age and account for environmental and other influences and suggest that it could be a universal age marker.

Researchers led by Erasmus MC Cancer Institute's John Martens found circular RNAs to be abundant within primary breast cancer samples. They analyzed RNA-seq data from 348 primary breast cancers to identify 95,843 circRNAs, about 20 percent of which were recurrent. They confirmed three of the circRNAs they uncovered — RERE, CNOT2, and CREBBP — in a separate set of samples. Knocking down circCNOT2, they report, decreased the viability of two breast cancer cell lines, which the researchers say highlights the biological importance of these circRNAs. They additionally report that circCNOT2 levels, but not linear CNOT2 levels, could predict progression-free survival time among advanced breast cancer patients on aromatase inhibitor therapy.