ArticleNucleic acids research2012
Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
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Who cites it
95 citing papers in PubMed.
- 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
- Article
- HIV-1-encoded circular RNA enhances viral transcription through Tat binding.Nature microbiology · 2026Article
- Neuroinflammation and NeuroHIV: understanding the role of HIV-1 related factors in microglial activation.Translational psychiatry · 2026Review
- RNA splicing patterns contribute to burst size variation among HIV-1-infected Jurkat cell clones.Journal of virology · 2025Article
- High-resolution HIV-1 mNAR genomics and bioinformatics · 2025Article
- Comprehensive Transcriptome Annotation of Thousands of HIV-1 Genomes.bioRxiv : the preprint server for biology · 2025Article
- 5' cap sequestration is required for sensing of unspliced HIV-1 RNA by MDA5.bioRxiv : the preprint server for biology · 2025Article
- MrHAMER2: high-accuracy long-read RNA sequencing to decode isoform-specific variation in viral transcripts during latency.bioRxiv : the preprint server for biology · 2025Article
- The translational landscape of HIV-1 infected cells reveals key gene regulatory principles.Nature structural & molecular biology · 2025Article
- Non-AUG HIV-1 uORF translation elicits specific T cell immune response and regulates viral transcript expression.Nature communications · 2025Article
- Article
- Optimization of a lentivirus-mediated gene therapy targeting HIV-1 RNA to eliminate HIV-1-infected cells.Molecular therapy. Nucleic acids · 2024Article
- piRNA Defense Against Endogenous Retroviruses.Viruses · 2024Review
- Article
- Translation of HIV-1 unspliced RNA is regulated by 5' untranslated region structure.Journal of virology · 2024Article
- Review
- Global m6A methylation and gene expression patterns in human microglial HMC3 cells infected with HIV-1.Heliyon · 2023Article
- Nano-DMS-MaP allows isoform-specific RNA structure determination.Nature methods · 2023Article
- Clonally expanded HIV-1 proviruses with 5'-leader defects can give rise to nonsuppressible residual viremia.The Journal of clinical investigation · 2023Article
35 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
Alternative RNA splicing greatly expands the repertoire of proteins encoded by genomes. Next-generation sequencing (NGS) is attractive for studying alternative splicing because of the efficiency and low cost per base, but short reads typical of NGS only report mRNA fragments containing one or few splice junctions. Here, we used single-molecule amplification and long-read sequencing to study the HIV-1 provirus, which is only 9700 bp in length, but encodes nine major proteins via alternative splicing. Our data showed that the clinical isolate HIV-1(89.6) produces at least 109 different spliced RNAs, including a previously unappreciated ∼1 kb class of messages, two of which encode new proteins. HIV-1 message populations differed between cell types, longitudinally during infection, and among T cells from different human donors. These findings open a new window on a little studied aspect of HIV-1 replication, suggest therapeutic opportunities and provide advanced tools for the study of alternative splicing.
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