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Genome Research Papers on Viral Genomes, Brain RNA Interactions in Autism, More

Researchers from the University of Hawaii, Oxford Nanopore Technologies, and elsewhere outline a sequencing strategy for pulling viral genomes out of metagenomic sequence collections. The amplification- and assembly-free method is designed to directly sequence environmental viruses with single-molecule, nanopore sequencing reads that extend across complete viral genomes, the team explains, taking advantage of known virus and phage features. The authors applied a phage-finding pipeline to marine metagenomic sequences, for example, putting together thousands of draft virus genomes. "Our new virus sequencing strategy can provide previously unavailable information about the genome structures, population biology, and ecology of naturally occurring viruses and viral parasites," they write.

A team from Taiwan and the US takes a look at RNA-related regulatory shifts in individuals with autism spectrum disorder (ASD), focusing on circular RNAs and their interactions in post-mortem brain samples from dozens of individuals with or without ASD. Using RNA-seq data, the researchers assessed circular RNA (circRNA), microRNA, and messenger RNA interactions in more than 200 frontal cortex, temporal cortex, or cerebellar vermis samples from 48 ASD-affected individuals and 49 unaffected controls. Their search highlighted 60 circRNAs and related expression modules that were altered in ASD, along with almost 8,200 altered RNA interactions and potential gene and pathway targets of ASD-related regulatory networks. "To the best of our knowledge, this is the first systems-level view of [the] landscape of circRNA regulatory networks in ASD cortex samples," the authors report, noting that results so far "support a role for circRNA dysregulation and the corresponding circRNA-microRNA-mRNA axes in ASD pathophysiology."

Finally, investigators in the US, Brazil, Japan, and Russia present human gene expression and transcriptome features found by analyzing data for from the FANTOM-CAGE-associated transcriptome (FANTOM-CAT) study with insights from a comprehensive "recount2" RNA sequence set that spans trillions of reads from tens of thousands of samples in available databases. The resulting expression atlas, dubbed FANTOM-CAT/recount2 (FC-R2), currently houses data representing almost 110,000 human coding and non-coding genes, the team says, making it possible to profile long non-coding RNAs and other transcripts in samples from individuals with or without disease. The authors relied on the recount2 re-quantified transcript data to find potential non-coding tumor contributors across more than a dozen cancer types, for example, and demonstrated still other possible applications of the FC-R2 atlas.