Genome-scale deconvolution of RNA structure ensembles

Morandi, Edoardo; Manfredonia, Ilaria; Simon, Lisa Marie; Anselmi, Francesca; Hemert, Martijn J. van; Oliviero, Salvatore; Incarnato, Danny

doi:10.1038/s41592-021-01075-w

Cited by 98 publications

(130 citation statements)

References 23 publications

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“…Moreover, subsequent covariation analysis using R-scape 43 (see Methods) detects 2 strong covarying base pairs (colored by nucleotide in Fig. 2, i.e., green A, blue U, orange C, and red G), also found in the phylogenetic analysis by Andrews et al 24 20,[30][31][32][33] and is also predicted by our SHAPE probing here for 156 and 222 nt constructs (see Comparison section). We see that AS1 is only conserved in Sarbecoviruses, with many deletions in the 5 strand in distant coronaviruses, and only a weak covarying base pair is found.…”

Section: Multiple Sequence Alignment and Variant Analysis Of Coronaviruses Emphasize Fse Featuressupporting

confidence: 80%

“…The in vitro DMS probing in Fig. S16C 29,31,32 again shows poor data alignment. These comparisons argue for a unified approach as performed in this study.…”

Section: Resultsmentioning

confidence: 98%

“…Here we focus on better understanding of this FSE conformational landscape using a combination of complementary graph-based modeling and chemical reactivity experiments. Already, several groups have explored FSE structure by modeling, [21][22][23][24][25] in vivo Selective 2 -Hydroxyl Acylation by Primer Extension (SHAPE) 26,27 and DMS structure probing experiments, 20,[28][29][30][31][32][33][34] NMR, 35 Cryo-EM, 29,36 and other biophysical mutational profiling and scanning experiments. 15,37,38 Many have characterized the FSE as a 3-stem H-type pseudoknot with colinear Stems 1 and 2 intertwined via a pseudoknot and perpendicular Stem 3.…”

Section: Introductionmentioning

confidence: 99%

“…However, depending on the modeling software and experimental technique, alternative secondary structures have been offered for SARS-CoV-2, both pseudoknotted and unknotted (see below). 20,[23][24][25][28][29][30][31][32][33][34] In our prior work 22 (see also commentary 39 ), we defined target residues for drug binding and gene editing of the FSE from designed minimal mutants that dramatically transform the FSE conformation. Our RAG (RNA-As-Graphs) machinery represents RNA 2D structure as coarse-grained dual graphs, where doublestranded RNA helices are represented as vertices, and loop strands are edges.…”

Section: Introductionmentioning

confidence: 99%

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To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element

Schlick

Zhu

Dey

et al. 2021

Preprint

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The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG" (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure, is replaced by a different, HL-type 3-stem pseudoknot (3_3) as more residues, in particular the slippery site's 7 residues, are considered. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribosome during translation. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.

show abstract

Section: Multiple Sequence Alignment and Variant Analysis Of Coronaviruses Emphasize Fse Featuressupporting

confidence: 80%

“…The in vitro DMS probing in Fig. S16C 29,31,32 again shows poor data alignment. These comparisons argue for a unified approach as performed in this study.…”

Section: Resultsmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

To knot or not to knot: Multiple conformations of the SARS-CoV-2 frameshifting RNA element

Schlick

Zhu

Dey

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Many sequences, including riboswitches, mRNAs and lncRNAs [9] , are expected to fold into a variety of competing structures that can coexist. To account for this structural diversity, several methods have been recently developed that allow studying alternative RNA conformations using experimental data [17] , [18] , [19] , [20] , [21] .…”

Section: Introductionmentioning

confidence: 99%