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This Week in PNAS: Nov 20, 2018

In the Proceedings of the National Academy of Sciences, a team from Yale University introduces an analytical method for analyzing the expression of endogenous retroviruses (ERV) in a range of cell types. The bioinformatic tool, known as ERVmap, brings RNA sequence data together with information on more than 3,200 annotated human proviral ERVs, the researchers say. They applied ERVmap to a range of cell line and primary cell types, uncovering ERVs with expression shifts in one or more cell or tissue types in systemic lupus erythematosus or breast cancer. "ERVmap can be used with any RNA sequencing data to potentially reveal novel ERV antigens and proteins involved in diseases such as cancer, neurodegenerative diseases, infectious diseases, and autoimmunity," the authors report.

Researchers from the University of Chicago and elsewhere explore apparent ties between the non-coding chromosome 1 variant rs17114036 — previously proposed as protective in coronary artery disease and ischemic stroke risk — and the blood flow-mediated regulation of human aortic endothelial cell activity. The team used chromatin immunoprecipitation sequencing, ATAC-seq, chromatin accessibility quantitative trait locus mapping, CRISPR-based gene editing, and other approaches to characterize rs17114036 activity in human aortic endothelial cells, identifying blood flow-related transcription factor binding and enhancer activity at the SNP site. "The molecular insights suggest that human genetic variants provide a layer of molecular control by which cells convert physical stimuli in biological signaling via tissue-specific enhancers," they write. 

A National Cancer Institute-led team describes circular RNAs (circRNA) that appear to influence interactions between human hosts and viruses such as Kaposi sarcoma herpesvirus. Using array-based expression profiling, circRNA sequencing, and other approaches, the researchers assessed circRNA patterns in human endothelial or B cell lines infected with KSHV, uncovering human circRNAs with altered expression in response to KSHV infection, including circRNAs with potential antiviral activity, as well as circRNAs encoded by the virus itself. "We discovered a new layer of host-virus interactions with circRNAs which are potentially applicable to other viruses," they write, "and these antiviral circRNAs or viral circRNAs may represent novel therapeutic targets."