Show simple item record

dc.creatorMagalis, Brittany Rife
dc.creatorPond, Sergei L Kosakovsky
dc.creatorSummers, Michael F
dc.creatorSalemi, Marco
dc.date.accessioned2021-01-21T15:54:23Z
dc.date.available2021-01-21T15:54:23Z
dc.date.issued2018-01
dc.identifier.issn2057-1577
dc.identifier.issn2057-1577
dc.identifier.doihttp://dx.doi.org/10.34944/dspace/4809
dc.identifier.otherGL3GM (isidoc)
dc.identifier.other29951250 (pubmed)
dc.identifier.urihttp://hdl.handle.net/20.500.12613/4827
dc.description.abstractLentiviral RNA genomes contain structural elements that play critical roles in viral replication. Although structural features of 5'-untranslated regions have been well characterized, attempts to identify important structures in other genomic regions by Selective 2'-Hydroxyl Acylation analyzed by Primer Extension (SHAPE) have led to conflicting structural and mechanistic conclusions. Previous approaches accounted neither for sequence heterogeneity that is ubiquitous in viral populations, nor for selective constraints operating at the protein level. We developed an approach that augments SHAPE with phylogenetic analyses and applied it to investigate structure in coding regions (cRNA) within the HIV and SIV envelope genes. Analysis of single-genome SHAPE data with phylogenetic information from diverse lentiviral sequences argues against the conservation of a putative global gp120 RNA structure but points to the existence of core RNA sub-structures. Our findings establish a framework for considering sequence heterogeneity and protein function in de novo RNA structure inference approaches.
dc.format.extentvey018-
dc.language.isoen
dc.relation.haspartVIRUS EVOLUTION
dc.relation.isreferencedbyOxford University Press (OUP)
dc.rightsCC BY-NC
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/
dc.subjectHIV
dc.subjectSIV
dc.subjectRNA structure
dc.subjectevolution
dc.subjectSHAPE
dc.subjectphylogenetics
dc.titleEvaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts
dc.typeArticle
dc.type.genreJournal Article
dc.relation.doi10.1093/ve/vey018
dc.ada.noteFor Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.edu
dc.creator.orcidPond, Sergei L. Kosakovsky|0000-0003-4817-4029
dc.date.updated2021-01-21T15:54:19Z
refterms.dateFOA2021-01-21T15:54:23Z


Files in this item

Thumbnail
Name:
Evaluation of global HIVSIV ...
Size:
1.549Mb
Format:
PDF

This item appears in the following Collection(s)

Show simple item record

CC BY-NC
Except where otherwise noted, this item's license is described as CC BY-NC