A map of the SARS-CoV-2 RNA structurome

Abstract

SARS-CoV-2 has exploded throughout the human population. To facilitate efforts to gain insights into SARS-CoV-2 biology and to target the virus therapeutically, it is essential to have a roadmap of likely functional regions embedded in its RNA genome. In this report, we used a bioinformatics approach, ScanFold, to deduce the local RNA structural landscape of the SARS-CoV-2 genome with the highest likelihood of being functional. We recapitulate previously-known elements of RNA structure and provide a model for the folding of an essential frameshift signal. Our results find that SARS-CoV-2 is greatly enriched in unusually stable and likely evolutionarily ordered RNA structure, which provides a large reservoir of potential drug targets for RNA-binding small molecules. Results are enhanced via the re-analyses of publicly-available genome-wide biochemical structure probing datasets that are broadly in agreement with our models. Additionally, ScanFold was updated to incorporate experimental data as constraints in the analysis to facilitate comparisons between ScanFold and other RNA modelling approaches. Ultimately, ScanFold was able to identify eight highly structured/conserved motifs in SARS-CoV-2 that agree with experimental data, without explicitly using these data. All results are made available via a public database (the RNAStructuromeDB: https://structurome.bb.iastate.edu/sars-cov-2) and model comparisons are readily viewable at https://structurome.bb.iastate.edu/sars-cov-2-global-model-comparisons.

To Knot or Not to Knot: Multiple Conformations of the SARS-CoV-2 Frameshifting RNA Element

“…We see that Stem 1 is highly conserved, with deletions in the 3′ strand in only one distant coronavirus. Moreover, subsequent covariation analysis using R-scape 43 (see Methods ) detects 2 strong covarying base pairs (colored by nucleotide in Figure 2 , i.e., green A, blue U, orange C, and red G), also found in the phylogenetic analysis by Andrews et al 24 Many deletions are found in Stem 3 and the sequences are less conserved, suggesting different locations and lengths for Stem 3 in different coronaviruses. Stem 2 is the shortest and the most flexible.…”

“…Several works have experimentally scanned RNA genomes with windows of variable lengths. 24 , 37 , 46 In secondary structure predictions of RNAs, 120 nt is considered reasonable for predictions. 47 , 48 Indeed, in our application of five 2D folding programs that can predict pseudoknots (PKNOTS, 49 NUPACK, 50 IPknot, 51 ProbKnot, 52 and vsfold5 53 ) to four RNAs with pseudoknots, we find that the 120 nt window recommended in the literature appears reasonable in general ( Figure S3 ).…”

“…It is dominant in two studies using sequence length 81 nt 25 and 123 nt. 24 Both groups use a 2D program which cannot predict pseudoknots, RNAfold. 61 …”

SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes

“…2C); this stability value is found to be unusually low given the AU-rich nucleotide composition, suggesting that it arose through an evolutionarily-driven process; indeed, the thermodynamic Z-score was -5.5 (meaning that the WT sequence is more than 5 standard deviations more stable than random). In addition, a comprehensive analysis of RNA structural motifs in SARS-CoV-2 found that this hairpin is one of the few (nine) that show evidence of statistically significant sequence covariation — a feature of evolutionary conservation (21). The formation of the hairpin is also in agreement with previously-reported structure probing reactivity datasets (22-25), where the only reactive nucleotides occur in loop regions.…”

“…B) Location of vmiR-5p and viRNA-3p annotated on an alignment of coronavirus reference sequences. The hairpin base pairs are indicated by arcs above the sequence alignment with the two previously identified covarying base pairs (21) indicated in green. Alignment and base pairs visualized using the program R-CHI (76).…”