Divide and conquer: antiviral restriction of #influenza A virus
by a novel ISG15 spliceform by
@sfbkr.bsky.social
and Co...the plot thickens #genesInPieces
www.biorxiv.org/content/10.6...
@biorxivpreprint.bsky.social

@biorxiv-microbiol.bsky.social

Proud to be in a class with some seriously impressive up-and-comers. Inaugural class here: journals.asm.org/journal/jvi/...

I'll be penning an article with colleague and friend @hanckslab.bsky.social on mitochondrial proteins that moonlight to execute immune responses

@jvico-eics.bsky.social

A subclass of small RNAs is encoded by exons of protein-coding genes - BMC Genomics Background Small RNAs regulate gene expression in species across the tree of life. miRNAs, which impact a variety of cellular and physiological processes ranging from development and stress adaptation to host defense, are one of the best characterized classes of small RNA. Many miRNAs are produced from longer non-coding transcripts generated from host genes via a series of RNA cleavage reactions. The location of a small RNA within a host gene can shape the processing of the mature small RNA. For example, a type of miRNAs derived from host gene intronic sequence, referred to as miRtrons, are Drosha-independent and reliant on splicing for biogenesis. Relatedly, processing of a small RNA from an exon of a protein-coding mRNA, in principle, may destabilize it and compromise translation of the host gene. Prior to extensive transcriptome analysis, informatics analyses identified six human miRNAs embedded in exons of protein-coding genes and experimental studies have characterized additional anecdotal examples. Still, whether protein-coding mRNAs encoding small RNAs represent an appreciable class of host genes given the now recognized complexity of the transcriptome is unclear. Results Our analysis finds 201 small RNAs (118 human and 83 mouse) encoded by expressed exons of protein-coding genes (5’-UTR, CDS, 3’-UTR). Forty-six of these cases (29 human and 17 mouse) are also present in MirGeneDB which includes the most up-to-date miRNA classifications. Many of these small RNAs are poorly characterized with 96% of the protein-coding host gene relationships identified here not previously known. Furthermore, the identification of nearly fifty human and mouse small RNAs embedded within coding exons of canonical ORFs suggests that overlapping hybrid genes might be more common than previously appreciated in higher organisms. Expression analysis for a subset of these small RNAs indicates that many display differential expression across human tissues with the pattern correlating significantly with the expression of the candidate protein-coding host gene. Significance Overall, our analysis suggests that the number of protein-coding transcripts serving as host genes is greater than previously recognized. Our small RNA host gene classifications may serve as a resource to shed new light on small RNA biology, specific host genes, and gene regulation.

Switches: New..lots of protein-coding mRNAs encode #miRNA ..former Ph.D. student's last hurrah building on our #mitochondria C15orf48/miR-147b stuff bmcgenomics.biomedcentral.com/articles/10....

Lab first, #cookies, to kick off the new academic year...stay tuned #mitochondria

Tandem split-GFP influenza A viruses for sensitive and accurate replication analyses Reporter influenza A viruses (IAVs) are valuable tools for studying virus fitness, screening antivirals, and assessing host-virus interactions. However, the compact and segmented nature of the IAV gen...

shine bright: sweet new set of flu gfp reporter viruses from @sfbkr.bsky.social
biorxiv.org/content/10.1...

a bald man in a blue suit is making a face . ALT: a bald man in a blue suit is making a face .

Preprint on tandem split-GFP influenza viruses is now up! We strung 7 copies of GFP11 together to make a bright virus with minimal fitness defects. Fluorescence requires GFP1-10 from cells, so we made a few that are relevant for flu. See this fluorescent love story: www.biorxiv.org/cgi/content/...

Drawing of a cell showing mitochondria in the cytoplasm, with murine norovirus virions exiting the cell through damage to the plasma membrane. Image credit: Valerie Rodriguez Irizarry

Photo of Valerie Rodriguez Irizarry

Valerie Rodriguez Irizarry’s tour de force paper on murine norovirus adaptation/egress is now out in peer-reviewed form ‪@plosbiology.org‬. It highlights the power of forward genetics in virology research. 🧵 1/10 journals.plos.org/plosbiology/...

Gag proteins encoded by endogenous retroviruses are required for zebrafish development | PNAS Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. ...

💥🥳 At long last, our latest paper is out!

Gag proteins of endogenous retroviruses are required for zebrafish development

www.pnas.org/doi/10.1073/...

Led heroically by Sylvia Chang & @jonowells.bsky.social

A study which has changed the way I think of #transposons! No less! 🧵 1/n

Viral piracy of host RNA phosphatase DUSP11 by avipoxviruses Author summary Viruses face a critical challenge of disabling or avoiding host immune defenses. Cells typically recognize the presence of a virus through specific molecular markers, including triphosp...

Newest: Virologs mark #RNA metabolism as an evolutionary battleground during infection - Great collaboration w/@sullivanlab.bsky.social & Kayla Szymanik @plos.org journals.plos.org/plospathogen...

Viral piracy of host RNA phosphatase DUSP11 by avipoxviruses Author summary Viruses face a critical challenge of disabling or avoiding host immune defenses. Cells typically recognize the presence of a virus through specific molecular markers, including triphosp...

Previously, KO and overexpression showed host RNA 5’ triphosphatase DUSP11 can reduce RIG-I sensitivity.

Here, we show poxviruses code for viral DUSP11 that can regulate host RNP III transcripts and RIG-I, providing evolutionary support DUSP11 can be pro-viral.

journals.plos.org/plospathogen...

Viral piracy of host RNA phosphatase DUSP11 by avipoxviruses Author summary Viruses face a critical challenge of disabling or avoiding host immune defenses. Cells typically recognize the presence of a virus through specific molecular markers, including triphosp...

Viral piracy of host RNA phosphatase DUSP11 by avipoxviruses

journals.plos.org/plospathogen...