ArticleNucleic acids research2001
Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3' splice site and its cis-regulatory element: possible involvement in RNA splicing.
Article in Nucleic acids research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 79 citations in OpenAlex.
- Cooperative Binding of SRSF3 to Structured 3'ss-α Exon RNA during α Exon Inclusion in the ZO-1 mRNA.Current issues in molecular biology · 2023Article
- Structural and Functional RNA Motifs of SARS-CoV-2 and Influenza A Virus as a Target of Viral Inhibitors.International journal of molecular sciences · 2023Review
- Review
- Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for Differential Binding of hnRNP Splicing Auxiliary Factors.Journal of molecular biology · 2022Article
- Plasma-Derived HIV-1 Virions Contain Considerable Levels of Defective Genomes.Journal of virology · 2022Article
- Conserved long-range base pairings are associated with pre-mRNA processing of human genes.Nature communications · 2021Article
- Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection.Retrovirology · 2020Article
- Tat IRES modulator of tat mRNA (TIM-TAM): a conserved RNA structure that controls Tat expression and acts as a switch for HIV productive and latent infection.Nucleic acids research · 2020Article
- A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance.PLoS computational biology · 2019Article
- Alternative splicing of U2AF1 reveals a shared repression mechanism for duplicated exons.Nucleic acids research · 2017Article
- Production of HIV-1Frontiers in microbiology · 2017Article
- HIV-1 Vpr N-terminal tagging affects alternative splicing of the viral genome.Scientific reports · 2016Article
- Natural Single-Nucleotide Variations in the HIV-1 Genomic SA1prox Region Can Alter Viral Replication Ability by Regulating Vif Expression Levels.Journal of virology · 2016Article
- Article
- Identification of U2AF(35)-dependent exons by RNA-Seq reveals a link between 3' splice-site organization and activity of U2AF-related proteins.Nucleic acids research · 2015Article
- Strong epistatic selection on the RNA secondary structure of HIV.PLoS pathogens · 2014Article
- Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation.Human molecular genetics · 2014Article
- The influenza A segment 7 mRNA 3' splice site pseudoknot/hairpin family.RNA biology · 2012Article
- The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin.PloS one · 2012Article
- Structural and functional analysis of the Rous Sarcoma virus negative regulator of splicing and demonstration of its activation by the 9G8 SR protein.Nucleic acids research · 2011Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
The HIV-1 transcript is alternatively spliced to over 30 different mRNAs. Whether RNA secondary structure can influence HIV-1 RNA alternative splicing has not previously been examined. Here we have determined the secondary structure of the HIV-1/BRU RNA segment, containing the alternative A3, A4a, A4b, A4c and A5 3' splice sites. Site A3, required for tat mRNA production, is contained in the terminal loop of a stem-loop structure (SLS2), which is highly conserved in HIV-1 and related SIVcpz strains. The exon splicing silencer (ESS2) acting on site A3 is located in a long irregular stem-loop structure (SLS3). Two SLS3 domains were protected by nuclear components under splicing condition assays. One contains the A4c branch points and a putative SR protein binding site. The other one is adjacent to ESS2. Unexpectedly, only the 3' A residue of ESS2 was protected. The suboptimal A3 polypyrimidine tract (PPT) is base paired. Using site-directed mutagenesis and transfection of a mini-HIV-1 cDNA into HeLa cells, we found that, in a wild-type PPT context, a mutation of the A3 downstream sequence that reinforced SLS2 stability decreased site A3 utilization. This was not the case with an optimized PPT. Hence, sequence and secondary structure of the PPT may cooperate in limiting site A3 utilization.
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