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This Week in Nucleic Acids Research: Feb 14, 2018

Researchers from the University of North Carolina at Chapel Hill explore genomic structure diversity in mosquito-borne alphaviruses with a method called "selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling," or SHAPE-MaP. The team focused on the Sindbis virus and the Venezuelan equine encephalitis virus, using SHAPE-MaP to uncover widespread structural element diversity among alphaviruses. "Our data suggest that alphavirus RNA genomes are highly divergent structurally despite similar genomic architecture and sequence conservation," the authors note, adding that "RNA structural elements are critical to the viral life cycle." 

A team from South Korea introduces an automated, standalone web application to retrieve and examine large sets of publicly available next-generation sequence data for transcriptomic and epigenomic analyses. The pipeline, called Octopus-toolkit, brings together and processes publicly available RNA sequence, ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, and MNase-seq for a range of organisms — from humans to yeast, fruit flies, mice, and dogs, the researchers say. For example, they applied the Octopus-toolkit to STAT5 transcription factor data from several mouse tissues, as well as Saccharomyces cerevisiae datasets related to histone modifying complex recruitment in the yeast. The authors say the approach "will be useful for users who are willing to mine the many epigenomics and transcriptomic treasures that are publicly hidden as more data becomes available."

Finally, investigators from Stanford University and elsewhere introduce a high-throughput assay for detecting SNPs using sequencing-based mismatch detection clues. The Diff-seq strategy "leverages the Surveyor endonuclease to cleave mismatched DNA molecules that are generated after cross-annealing a complex pool of DNA fragments," the team explains. "Sequencing libraries enriched for Surveyor-cleaved molecules result in increased coverage at the variant sites." For their proof-of-principle analysis, the researchers applied Diff-seq to a vector fragment with known variants and to evolving HIV clones collected from the same individual before and after treatment, where it appeared more adept at detecting sparsely spaced than tightly packed SNPs.