ArticleRNA (New York, N.Y.)2008
Evidence of a novel RNA secondary structure in the coding region of HIV-1 pol gene.
Article in RNA (New York, N.Y.), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 22 citations in OpenAlex.
- Light-regulated microRNAs shape dynamic gene expression in the zebrafish circadian clock.PLoS genetics · 2025Article
- Synonymous Variants of Uncertain Silence.International journal of molecular sciences · 2023Article
- Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication.Microbiology and molecular biology reviews : MMBR · 2022Review
- Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure.Virus evolution · 2022Article
- Structural Context of a Critical Exon of Spinal Muscular Atrophy Gene.Frontiers in molecular biosciences · 2022Review
- A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance.PLoS computational biology · 2019Article
- New windows into retroviral RNA structures.Retrovirology · 2018Review
- Global synonymous mutagenesis identifies cis-acting RNA elements that regulate HIV-1 splicing and replication.PLoS pathogens · 2018Article
- Evidence of translation efficiency adaptation of the coding regions of the bacteriophage lambda.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Mechanistic and Kinetic Differences between Reverse Transcriptases of Vpx Coding and Non-coding Lentiviruses.The Journal of biological chemistry · 2015Article
- Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain.Nucleic acids research · 2015Article
- Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes.PLoS computational biology · 2015Article
- Widespread signatures of local mRNA folding structure selection in four Dengue virus serotypes.BMC genomics · 2015Article
- Unmasking the information encoded as structural motifs of viral RNA genomes: a potential antiviral target.Reviews in medical virology · 2013Review
- Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs.PLoS pathogens · 2013Article
- Evolutionary evidence for alternative structure in RNA sequence co-variation.PLoS computational biology · 2013Article
- Genetic features of cerebrospinal fluid-derived subtype B HIV-1 tat.Journal of neurovirology · 2012Article
- Structural effects of linkage disequilibrium on the transcriptome.RNA (New York, N.Y.) · 2012Article
- APOBEC3G-induced hypermutation of human immunodeficiency virus type-1 is typically a discrete "all or nothing" phenomenon.PLoS genetics · 2012Article
- The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA.Nucleic acids research · 2009Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
RNA secondary structures play several important roles in the human immunodeficiency virus (HIV) life cycle. To assess whether RNA secondary structure might affect the function of the HIV protease and reverse transcriptase genes, which are the main targets of anti-HIV drugs, we applied a series of different computational approaches to detect RNA secondary structures, including thermodynamic RNA folding predictions, synonymous variability analysis, and covariance analysis. Each method independently revealed strong evidence of a novel RNA secondary structure at the junction of the protease and reverse transcriptase genes, consisting of a 107-nucleotide region containing three stems, A, B, and C. First, RNA folding calculations by mfold and RNAfold both predicted the secondary structure with high confidence. Moreover, the same structure was predicted in a diverse set of reference sequences in HIV-1 group M, indicating that it is conserved across this group. Second, the predicted base-pairing regions displayed markedly reduced synonymous variation (approximately threefold lower than average) in a data set of 20,000 HIV-1 subtype B sequences from clinical samples. Third, independent analysis of covariation between synonymous mutations in this data set identified 10 covariant mutation pairs forming two diagonals that corresponded exactly to the sites predicted to base-pair in stems A and B. Finally, this structure was validated experimentally using selective 2'-hydroxyl acylation and primer extension (SHAPE). Discovery of this novel secondary structure suggests many directions for further functional investigation.
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Registered trials
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