About: Genome-wide mapping of therapeutically-relevant SARS-CoV-2 RNA structures

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About: Genome-wide mapping of therapeutically-relevant SARS-CoV-2 RNA structures Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Genome-wide mapping of therapeutically-relevant SARS-CoV-2 RNA structures
Creator	Ogando, Natacha Van Hemert, Martijn Bujnicki, Janusz Ghosh, Chandran, Nithin Incarnato, Danny Manfredonia, Ilaria Marinus, Tycho Ponce-Salvatierra, Snider, Eric Wirecki, Tomasz
Source	BioRxiv
abstract	SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome of ∼30 kb, whose outbreak caused the still ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally conserved structural elements within coronavirus RNA genomes have been identified to date. Here, we performed RNA structure probing by SHAPE-MaP to obtain a single-base resolution secondary structure map of the full SARS-CoV-2 coronavirus genome. The SHAPE-MaP probing data recapitulate the previously described coronavirus RNA elements (5′ UTR, ribosomal frameshifting element, and 3′ UTR), and reveal new structures. Secondary structure-restrained 3D modeling of highly-structured regions across the SARS-CoV-2 genome allowed for the identification of several putative druggable pockets. Furthermore, ∼8% of the identified structure elements show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. In addition, we identify a set of persistently single-stranded regions having high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics. Collectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.
has issue date	2020-06-15(xsd:dateTime)
bibo:doi	10.1101/2020.06.15.151647
has license	biorxiv
sha1sum (hex)	b71069aed7e2cbcbcda664c33febdfd2e5b6487b
schema:url	https://doi.org/10.1101/2020.06.15.151647
resource representing a document's title	Genome-wide mapping of therapeutically-relevant SARS-CoV-2 RNA structures
schema:publication	bioRxiv
resource representing a document's body	covid:b71069aed7e2cbcbcda664c33febdfd2e5b6487b#body_text
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