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This Week in PNAS: Feb 2, 2016

In a study slated to appear in the early, online edition of the Proceedings of the National Academy of Sciences, researchers from Wayne State University and Indiana University explore the consequences of single-stranded cytosine deamination in Escherichia coli. Using whole-genome sequencing, the team tallied up the mutations that appeared over thousands of generations in mutant E. coli strains with diminished uracil repair activity that expressed the catalytic domain of a single-stranded DNA-specific cytosine deaminase enzyme called APOBEC3G. The study's authors note that cytosine to thymine deamination was more common on E. coli's lagging-strand DNA template than its leading strand, revealing clues to APOBEC3G activity and perhaps explaining some previously described base composition biases in microbial genomes.

A team from China and the US characterize two herpes simplex virus-1 microRNAs produced during late stages of a HSV-1 infection. With the help of deep sequencing on HSV-1-infected cell lines, the researchers identified these miRNAs — dubbed miR-H28 and miR-H29 — and followed their accumulation patterns and effects on viral messenger RNA during productive HSV-1 infections. From these and other experiments, the authors found that miR-H28 and miR-H29 appear during late stages of infection and are transported out of infected host cells via exosomes in a manner that's suspected of suppressing excessive HSV-1 replication and potentially boosting transmission from infected to uninfected hosts.

Brigham and Women's Hospital and Harvard Medical School researchers describe an updated version of a cross-linked affinity method called BioTAP-XL, a cross-linked tandem affinity pulldown method designed to assess interactions by proteins associated with chromatin. After making some tweaks to the BioTAP-XL protocol, the team applied it to Drosophila and human cells, where the approach showed promise for quantifying post-translational modifications such as histones, interacting chromatin partners, and non-histone proteins interacting in this network. "[W]e greatly extend the practicality of BioTAP-XL to enable comprehensive identification of protein complexes and their local chromatin environment," the investigators note.