RNA Genome Structure

Reviews to check

(Manfredonia 2021 PMID: 33367597)

PMID: 36348050 2022

Genome structure in the virion - RNA structure in the virion

Genome structures in cells - RNA structure in cells

Genome modifications at 5’ and 3’ end

The genomes 5′end is capped and has a 3′ poly(A) tail with short 5′and 3′ un-translated region sequences forming regulatory stem‐loop structures and a single leader sequence proximal to the 5′end.

Prediction of structure and long distance base pairing

(Lan 2020 doi: 10.1101/2020.06.29.178343) some RNA viruses contain known essential structures wherein bases over 300 nt apart are paired (e.g. the Rev response element in HIV-1 spans approximately 350 nt (Watts et al., 2009)).

• however: suggesting that long-distance (i.e. >120 nt) interactions across the SARS-CoV-2 RNA have a small effect on the identity of local structures.

PMID: 36192461 2022

visualiztion and comparison of RNA 3D structures

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Structured regions

(Manfredonia 2020 doi: 10.1101/2020.06.15.151647) in vitro SHAPE

• 55.5% of the SARS-CoV-2 genome is structured, in agreement with the observed fraction of low reactive residues as determined by SHAPE probing.
• a degree like ribosomal RNA!!
• 149 structure elements having both low SHAPE reactivities, reflecting low nucleotide dynamics (possibly due to base-pairing), and low Shannon entropies, reflecting high structural stability, thus the presence of a predominant RNA structural conformation. - these regions encompassed ~38.6% of the SARS-CoV-2 genome (11,547 bases) and included the 5′ and 3′ UTRs. These regions are likely to be involved in the mechanistic and structural aspects of the viral RNA function. -- from these 70 shorter structured elements were selected. Predicted stable RNA folds
• Previous computational analyses have shown that complex structured RNA molecules often exhibit pockets with physical properties suitable for small molecule binding, which can be identified in RNA 3D structure models (Hewitt et al., 2019). Thus, the discovery of multiple structured regions in SARS-CoV-2 genomic RNA offered an opportunity to test their potential to be targeted by small molecules.

(Lan 2020 doi: 10.1101/2020.06.29.178343) full-length in-vivoDMS-MaPseq on SARS-CoV2 infected cells.

• regions of potential interest in the SARS-CoV-2 genome, we identified all structured and accessible regions, which we define as stretches of at least 10 consecutive paired bases or 14 consecutive unpaired bases, respectively (Figure 2A).
• Structured regions could be functional elements of the genome that are potential targets of therapeutics. We identify 215 structured regions covering a total of 2,359 bases (8.5% of the genome).
• Predicted stable RNA folds

Single stranded regions

(Manfredonia 2020 doi: 10.1101/2020.06.15.151647) in vitro SHAPE

• targets for the design of antisense oligonucleotide (ASO) therapeutics.
• 70 such regions, at least 25 nucleotides long, spanning a total of 2,910 bases (9.7% of the SARS-CoV-2 genome) (Figure S5 and Table S2).
• Notably, ~23.9% of these regions, (2.4% of the SARS-CoV-2 genome), showed over 70% conservation in SARS-CoV (average ~81.3%) and over 50% conservation in the other three datasets
• Particularly, five regions (accounting for a total of 240 bases) showed exceptionally high conservation in all the analyzed alignments (average SARS-CoV: 86.4%; MERS-CoV: 78.6%; other Beta-CoV: 74.2%; all other CoV: 68.3%), suggesting that some essential regulatory RNA element might reside here and be under strong selection.

(Lan 2020 doi: 10.1101/2020.06.29.178343)

• Accessible regions in viral genomes are potential targets of antisense oligonucleotide therapeutics (Eckardt, Romby and Sczakiel, 1997; Ding, 2001; Rangan, Zheludev and Das, 2020) through the mechanism of RNA interference (Wilson and Doudna, 2013).
• We identify 261 accessible regions covering 6,305 bases (21% of the entire genome). As there are 11 such regions within ORF-N, which is present in every sgRNA, every sgRNA may be targetable with antisense oligos. Additionally, every open reading frame except ORF-E contains at least one of these predicted accessible regions, raising the possibility of targeting individual sgRNAs.
• stringent threshold of 25 consecutive nucleotides predicted to be unpaired, we find 78 accessible regions, one of which is located within ORF-N (34 nt, positions 28,721 - 28,754) and hence in every genomic and subgenomic RNA. The two longest stretches of consecutive predicted unpaired bases are both 122 nt long and occupy positions 9,602 - 9,723 (within ORF1a) and 21,573 - 21,694 (within ORF-S). These regions may offer multiple binding sites for antisense oligonucleotides.