Overview to RNA-SHAPE experiments in CoV2

SHAPE-map of CoV2 in cells

(PMID: 33444546 Pyle 2021)

• secondary structure of the SARS-CoV-2 RNA genome probed in infected cells.
• networks of well-folded RNA structures throughout Orf1ab
• new aspects of SARS-CoV-2 genome architecture that distinguish it from other single-stranded, positive-sense RNA viruses.
• we pinpoint individual regions of well-folded RNA structure that merit downstream functional analysis.
• analyzed using the ShapeMapper pipeline(Smola et al., 2015b).
• secondary structure prediction withthe SuperFoldpipeline(Smola et al., 2015b)

5' end shape corrasponds very well with the Iserman LLPS data (pmid: 32587965)

DMS on CoV2

(Lan 2020 doi: 10.1101/2020.06.29.178343) full-length in-vivoDMS-MaPseq on SARS-CoV2 infected cells. DMS rapidly and specifically modifies unpaired adenines and cytosines in vivo at their Watson-Crick faces.

• Combined, a total of ~1.58 million paired reads mapped to the coronavirus genome (Figure 1C), representing ~40% of total cellular RNA (post ribosomal RNA depletion).
• 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).
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in vitro SHAPE

(Iserman 2020 pmid: 32587965) + N binding ; LLPS

(Manfredonia 2020 doi: 10.1101/2020.06.15.151647) SHAPE-MaP analysis on ex vivo extracted and refolded SARS-CoV-2

• druggable pockets predicted
• 8% of the structures conserved among corona -> special function?