ArticlePLoS computational biology2015
Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- SHAPE-MaP-Based Assessment of the Structure of Citrus Tristeza Virus Long Non-Coding RNA.Viruses · 2026Article
- DEAD-box helicase intrinsically disordered domains and structural dynamics of HIV-1 RNA are required to reveal DDX3X catalytic efficiency.Nucleic acids research · 2025Article
- Structures of complete HIV-1 TAR RNA portray a dynamic platform poised for protein binding and structural remodeling.Nature communications · 2025Article
- e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features.Nucleic acids research · 2023Article
- In vivo secondary structural analysis of Influenza A virus genomic RNA.Cellular and molecular life sciences : CMLS · 2023Article
- Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RNA secondary structure packages evaluated and improved by high-throughput experiments.Nature methods · 2022Article
- Computational and Experimental Approaches to Study the RNA Secondary Structures of RNA Viruses.Viruses · 2022Review
- Stability and conformation of the dimeric HIV-1 genomic RNA 5'UTR.Biophysical journal · 2021Article
- Mapping the RNA structural landscape of viral genomes.Methods (San Diego, Calif.) · 2020Article
- CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent Mechanisms.Journal of virology · 2020Article
- Physical and Functional Analysis of Viral RNA Genomes by SHAPE.Annual review of virology · 2019Review
- A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance.PLoS computational biology · 2019Article
- Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies.Biochemistry · 2019Article
- RNA Structural Differentiation: Opportunities with Pattern Recognition.Biochemistry · 2019Review
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- The Effect of RNA Substitution Models on Viroid and RNA Virus Phylogenies.Genome biology and evolution · 2018Article
- New windows into retroviral RNA structures.Retrovirology · 2018Review
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3 authors.
Funding
Abstract
HIV and related primate lentiviruses possess single-stranded RNA genomes. Multiple regions of these genomes participate in critical steps in the viral replication cycle, and the functions of many RNA elements are dependent on the formation of defined structures. The structures of these elements are still not fully understood, and additional functional elements likely exist that have not been identified. In this work, we compared three full-length HIV-related viral genomes: HIV-1NL4-3, SIVcpz, and SIVmac (the latter two strains are progenitors for all HIV-1 and HIV-2 strains, respectively). Model-free RNA structure comparisons were performed using whole-genome structure information experimentally derived from nucleotide-resolution SHAPE reactivities. Consensus secondary structures were constructed for strongly correlated regions by taking into account both SHAPE probing structural data and nucleotide covariation information from structure-based alignments. In these consensus models, all known functional RNA elements were recapitulated with high accuracy. In addition, we identified multiple previously unannotated structural elements in the HIV-1 genome likely to function in translation, splicing and other replication cycle processes; these are compelling targets for future functional analyses. The structure-informed alignment strategy developed here will be broadly useful for efficient RNA motif discovery.
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