ArticleNature2009
Architecture and secondary structure of an entire HIV-1 RNA genome.
Article in Nature, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 548 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
548 citing papers in PubMed, 835 citations in OpenAlex.
- DMS-MaPseq and DREEM Analyses Implicate the Critical Role of RNA Structural Dynamics in Turnip Yellow Mosaic Virus Pathogenicity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Folding the message: mRNA structure as a regulatory layer of human mitochondrial gene expression.Biochimica et biophysica acta. Molecular cell research · 2026Review
- Article
- Modulating G-quadruplexes for therapeutic intervention: Structural diversity, stability, and emerging nucleic-acid-based strategies.Molecular therapy. Nucleic acids · 2026Review
- Transcription start site heterogeneity controls MDA5 sensing of unspliced HIV-1 RNAs.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Effect of TAR hairpin stabilization on HIV-1 reverse transcription.Journal of virology · 2026Article
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- VIRSE: a variational Bayesian framework for RNA structural ensemble inference.Briefings in bioinformatics · 2026Article
- Incorporation of genome-bound cellular proteins into HIV-1 particles regulates viral infection.Cell reports · 2026Article
- Diverse database and machine learning model to narrow the generalization gap in RNA structure prediction.Science advances · 2026Article
- RNA Structure Coordinates Translation Across the Meiotic Program.bioRxiv : the preprint server for biology · 2026Article
- Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers.Proteins · 2026Article
- Mapping the RNA Chaperone Activity of the Trypanosoma brucei Editosome Using SHAPE-Chemical Probing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Development of a Gene Therapy with Lentiviral Vectors for Spinocerebellar Ataxias.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Proteomic Characterization of HIV Infection.Advances in experimental medicine and biology · 2026Review
- High-resolution HIV-1 mNAR genomics and bioinformatics · 2025Article
- Aberrant strand transfer events across multiple stages of reverse transcription shape the heterogeneous landscape of the HIV-1 reservoir.Communications biology · 2025Article
- TVAE-RNA: ensemble-based RNA secondary structure prediction via transformer variational autoencoders.Bioinformatics (Oxford, England) · 2025Article
- Dynamical modeling and data analysis of HIV infection with infection-age, CTLs immune response and delayed antibody immune response.Journal of mathematical biology · 2025Article
- Expression of intron-containing HIV-1 RNA induces NLRP1 inflammasome activation in myeloid cells.PLoS biology · 2025Article
488 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Single-stranded RNA viruses encompass broad classes of infectious agents and cause the common cold, cancer, AIDS and other serious health threats. Viral replication is regulated at many levels, including the use of conserved genomic RNA structures. Most potential regulatory elements in viral RNA genomes are uncharacterized. Here we report the structure of an entire HIV-1 genome at single nucleotide resolution using SHAPE, a high-throughput RNA analysis technology. The genome encodes protein structure at two levels. In addition to the correspondence between RNA and protein primary sequences, a correlation exists between high levels of RNA structure and sequences that encode inter-domain loops in HIV proteins. This correlation suggests that RNA structure modulates ribosome elongation to promote native protein folding. Some simple genome elements previously shown to be important, including the ribosomal gag-pol frameshift stem-loop, are components of larger RNA motifs. We also identify organizational principles for unstructured RNA regions, including splice site acceptors and hypervariable regions. These results emphasize that the HIV-1 genome and, potentially, many coding RNAs are punctuated by previously unrecognized regulatory motifs and that extensive RNA structure constitutes an important component of the genetic code.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.