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This Week in Nucleic Acids Research: Jul 5, 2017

Pennsylvania State University researchers report on a method for discerning RNA structure across the genome, in vivo, at nucleotide-level resolution. The approach, known as Structure-seq2, builds on an earlier version of the method, but dials down byproduct formation and related ligation bias to subsequently bump up sensitivity, decrease required sample sizes, and improve coverage. The team applied Structure-seq2 to profile messenger RNA and ribosomal RNA in the rice species Oryza sativa. The authors note that the same strategies used for improving the original Structure-seq method may also enhance other existing strategies for profiling RNA structure genome-wide.

Investigators from the Smithsonian Institution's National Museum of Natural History, Pennsylvania State University, and elsewhere describe a high-throughput, shotgun sequencing-based strategy for establishing short tandem repeat (STR) markers in the absence of a corresponding reference genome. When the team applied its BaitSTR software pipeline to two diademed sifakas from an endangered rainforest lemur species in Madagascar, it was able to detect the set of 5,000 targeted STRs with between 97.3 percent and 99.6 percent success. A similar BaitSTR approach was subsequently used to take a look at STRs in fecal DNA samples from the same species.

Finally, a Tufts University team outlines a method for adapting single molecule array techniques to detect microRNAs digitally. Using a so-called sandwich assay based on a Simoa single molecular array method for detecting specific biomarkers, the researchers came up with an amplification-free approach for picking up a range of clinically relevant miRNAs present at low levels in a given sample. After demonstrating this approach in human serum spiked with synthetic miRNAs, they performed single molecule analyses of endogenous miRNAs found in total RNA samples. The study's authors argue that the approach "involves a simple workflow and delivers quantitative and highly sensitive results without reverse transcription or target amplification."