Description
This track shows data from Anna Pyle's lab at Yale University describing the RNA secondary
structure of the SARS-CoV-2 genome. The authors performed experimental
measurements using SHAPE (selective 2-hydroxyl acylation) as well as in-silico analysis.
These data are described in depth in
de Cesaris Araujo Tavares et al
and Huston, Wan, et al.
Display Conventions and Configuration
Two tracks are available:
SHAPE reactivity: A low SHAPE score (<0.4) indicates that the nucleotide is
not accessible (folded between complementary regions - base-paired). A mid
(0.4<SHAPE<0.85) or high SHAPE reactivity
(>0.85) indicates the nucleotide is flexible (single-stranded). A score of -999
means no data for that nucleotide was recovered experimentally. For
visualization purposes the minimum display value has been set to -0.5 and the
max has been set to 4.
Full Length Shannon Entropy: A genome-wide Shannon entropy profile derived from
base pairing probabilities was computed using SuperFold with in vivo SHAPE reactivity as
constraints . A low Shannon entropy (near 0) is evidence for well-determined RNA conformation.
Note that the authors provide further data (including secondary structure
predictions) at their github repository.
Methods
For Shannon entropy, comSuperFold was used with default settings to predict
secondary structure for the full-length SARS-CoV-2 RNA genome.
For
SHAPE_reactivity, VeroE6 cells were infected with 105 PFU of SARS133 CoV-2
isolate USA-WA1/2020. See the preprint
for further details.
wigToBigWig was used to convert wiggles from the author's github repository to bigWig files after filtering out headers.
The Github repository with all raw data files can be found here: https://github.com/pylelab/SARS-CoV-2_SHAPE_MaP_structure.
References
Huston NC, Wan H, Araujo Tavares RC, Wilen C, Pyle AM.
Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs
and mechanisms.
bioRxiv. 2020 Jul 10;.
PMID: 32676598; PMC: PMC7359520
Araujo Tavares RC, Mahadeshwar G, Pyle AM.
The global and local distribution of RNA structure throughout the SARS-CoV-2 genome.
bioRxiv. 2020 Jul 7;.
doi: 190660
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