2019
DOI: 10.1093/nar/gkz318
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In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs

Abstract: The influenza A virus (IAV) is a continuous health threat to humans as well as animals due to its recurring epidemics and pandemics. The IAV genome is segmented and the eight negative-sense viral RNAs (vRNAs) are transcribed into positive sense complementary RNAs (cRNAs) and viral messenger RNAs (mRNAs) inside infected host cells. A role for the secondary structure of IAV mRNAs has been hypothesized and debated for many years, but knowledge on the structure mRNAs adopt in vivo is currently missing. Here we sol… Show more

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Cited by 65 publications
(84 citation statements)
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“…Fortunately, a recent study acquired DMS profiles for influenza A mRNAs and E. coli ribosomal RNA with excellent signal-to-noise. 31 These data showed suppression of DMS signal at adenosines positioned at -5 within polyadenosine stretches (labeled 'Simon, 2019' in Fig. 2c), as did the original RMDB data studied in ref.…”
Section: Generality Of Anomalous Poly(a) Signal Across Prior Data Setssupporting
confidence: 65%
“…Fortunately, a recent study acquired DMS profiles for influenza A mRNAs and E. coli ribosomal RNA with excellent signal-to-noise. 31 These data showed suppression of DMS signal at adenosines positioned at -5 within polyadenosine stretches (labeled 'Simon, 2019' in Fig. 2c), as did the original RMDB data studied in ref.…”
Section: Generality Of Anomalous Poly(a) Signal Across Prior Data Setssupporting
confidence: 65%
“…However, we report here that the SARS-CoV-2 genomic RNA is nearly twice as compact and structured as HCV based on its folding stability, even when adjusting for its vastly greater overall length (~ 30 kb vs. ~10 kb). RNA structural motifs within the UTRs and ORFs of coronaviruses are seemingly larger and more complex than those observed in other virus families (Clyde and Harris 2006; Lim and Brown 2017;Li et al 2018;Simon et al 2019), suggesting that an understanding of coronavirus RNA structure will play a key role in understanding the mechanistic processes and vulnerabilities of this virus.…”
Section: Discussionmentioning
confidence: 96%
“…These ORFs are flanked on either side by a 5' and 3'UTR that have been shown in other coronaviruses to possess conserved RNA structures with important functional roles in the viral life cycle . Studies in Murine Hepatitis Virus (MHV) and Bovine Coronavirus (BCoV) suggest that the 5' viral termini folds in to 6 stems (SL1-SL6) that play roles in sgRNA synthesis context (Simon et al, 2019, Rouskin et al, 2014. Lan et al performed full-length in-vivo DMS-MaPseq on SARS-CoV2 infected cells (Lan et al, 2020b), but as DMS only reports on A and C nucleotides, the data coverage is necessarily sparse.…”
Section: Introductionmentioning
confidence: 99%