ArticleNucleic acids research2015
Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Distinguishing active HIV-1 infection from vaccine-induced seropositivity in HIV vaccine trial participants.Science advances · 2025Article
- Stability and conformation of the dimeric HIV-1 genomic RNA 5'UTR.Biophysical journal · 2021Article
- Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription.Journal of molecular biology · 2020Article
- A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance.PLoS computational biology · 2019Article
- Integrative modeling of the HIV-1 ribonucleoprotein complex.PLoS computational biology · 2019Article
- RNA secondary structure profiling in zebrafish reveals unique regulatory features.BMC genomics · 2018Article
- Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts.Virus evolution · 2018Article
- RNA structure inference through chemical mapping after accidental or intentional mutations.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Article
- HIV-1 Vpr N-terminal tagging affects alternative splicing of the viral genome.Scientific reports · 2016Article
- Stability of HIV Frameshift Site RNA Correlates with Frameshift Efficiency and Decreased Virus Infectivity.Journal of virology · 2016Article
- Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1.The Journal of biological chemistry · 2016Article
- Bridging the gap between in vitro and in vivo RNA folding.Quarterly reviews of biophysics · 2016Article
- Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic.PloS oneArticle
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7 authors.
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Abstract
A distance constrained secondary structural model of the ≈10 kb RNA genome of the HIV-1 has been predicted but higher-order structures, involving long distance interactions, are currently unknown. We present the first global RNA secondary structure model for the HIV-1 genome, which integrates both comparative structure analysis and information from experimental data in a full-length prediction without distance constraints. Besides recovering known structural elements, we predict several novel structural elements that are conserved in HIV-1 evolution. Our results also indicate that the structure of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping protein-coding regions the COS is supported by a particular high frequency of compensatory base changes, suggesting functional importance for this element. This new structural element potentially organizes the whole genome into three major domains protruding from a conserved core structure with potential roles in replication and evolution for the virus.
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