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Characterizing HIV-1 Splicing by Using Next-Generation Sequencing

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The D1-A2 and D2-A2 Pairs of Splice Sites from Human Immunodeficiency Virus Type 1 Are Highly Efficientin Vitro,in Spite of an Unusual Branch Site

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Two Strong 5′ Splice Sites and Competing, Suboptimal 3′ Splice Sites Involved in Alternative Splicing of Human Immunodeficiency Virus Type 1 RNA

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RNA Splice Site Utilization by Simian Immunodeficiency Viruses Derived from Sooty Mangabey Monkeys

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Influence of the Small Leader Exons 2 and 3 on Human Immunodeficiency Virus Type 1 Gene Expression

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Activation of a cryptic splice donor in human immunodeficiency virus type-1

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Functions of the auxiliary gene products of the human immunodeficiency virus type 1

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Regulation of mRNA accumulation by a human immunodeficiency virus trans-activator protein

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Regulation by HIV Rev depends upon recognition of splice sites

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The HIV-1 Rev Activation Domain is a nuclear export signal that accesses an export pathway used by specific cellular RNAs

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Nonsense-mediated mRNA decay: terminating erroneous gene expression

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Homologous SV40 RNA trans -splicing: Special case or prime example of viral RNA trans -splicing?

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Solution Structure of the HIV-1 Exon Splicing Silencer 3

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Modeling sequence evolution in acute HIV-1 infection

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Reverse transcriptase template switching and false alternative transcripts

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Heterologous HIV‐nef mRNA trans‐splicing: a new principle how mammalian cells generate hybrid mRNA and protein molecules

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Chapter 1 Regulation of HIV-1 Alternative RNA Splicing and Its Role in Virus Replication

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Thermodynamic and Phylogenetic Insights into hnRNP A1 Recognition of the HIV-1 Exon Splicing Silencer 3 Element

inferredcites →https://doi.org/10.1038/330489a0openalex-snapshot

Anti-termination of transcription within the long terminal repeat of HIV-1 by tat gene product

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Architecture and secondary structure of an entire HIV-1 RNA genome

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Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

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Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

inferredcites →https://doi.org/10.1074/jbc.270.41.24060openalex-snapshot

Inefficient Spliceosome Assembly and Abnormal Branch Site Selection in Splicing of an HIV-1 Transcript in Vitro

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Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1

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Biological and biochemical characterization of a cloned Leu-3- cell surviving infection with the acquired immune deficiency syndrome retrovirus.

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Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection

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The Complete Nucleotide Sequence of a Pathogenic Molecular Clone of Simian Immunodeficiency Virus

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SR proteins and hnRNP H regulate the splicing of the HIV‐1 tev‐specific exon 6D

inferredcites →https://doi.org/10.1093/nar/20.1.27openalex-snapshot

Structural features in TAR RNA of human and simian immunodeficiency viruses: a phylogenetic analysis

inferredcites →https://doi.org/10.1093/nar/gki185openalex-snapshot

Splicing of human immunodeficiency virus RNA is position-dependent suggesting sequential removal of introns from the 5' end

inferredcites →https://doi.org/10.1093/nar/gkm1147openalex-snapshot

Insights into the selective activation of alternatively used splice acceptors by the human immunodeficiency virus type-1 bidirectional splicing enhancer

inferredcites →https://doi.org/10.1093/nar/gks753openalex-snapshot

Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing

inferredcites →https://doi.org/10.1093/nar/gkv313openalex-snapshot

The HIV-1 Rev response element (RRE) adopts alternative conformations that promote different rates of virus replication

inferredcites →https://doi.org/10.1099/vir.0.000122openalex-snapshot

HIV-1 splicing is controlled by local RNA structure and binding of splicing regulatory proteins at the major 5′ splice site

inferredcites →https://doi.org/10.1126/science.1210460openalex-snapshot

NMR Detection of Structures in the HIV-1 5′-Leader RNA That Regulate Genome Packaging

inferredcites →https://doi.org/10.1126/science.aaa9266openalex-snapshot

Structure of the HIV-1 RNA packaging signal

inferredcites →https://doi.org/10.1128/jvi.01558-07openalex-snapshot

Negative and Positive mRNA Splicing Elements Act Competitively To Regulate Human Immunodeficiency Virus Type 1 Vif Gene Expression

inferredcites →https://doi.org/10.1128/jvi.02231-08openalex-snapshot

Regulation of vif mRNA Splicing by Human Immunodeficiency Virus Type 1 Requires 5′ Splice Site D2 and an Exonic Splicing Enhancer To Counteract Cellular Restriction Factor APOBEC3G

inferredcites →https://doi.org/10.1128/jvi.02660-07openalex-snapshot

Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing

inferredcites →https://doi.org/10.1128/jvi.59.2.284-291.1986openalex-snapshot

Production of acquired immunodeficiency syndrome-associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone

inferredcites →https://doi.org/10.1128/jvi.64.6.2505-2518.1990openalex-snapshot

A novel human immunodeficiency virus type 1 protein, tev, shares sequences with tat, env, and rev proteins

inferredcites →https://doi.org/10.1128/jvi.64.6.2519-2529.1990openalex-snapshot

Cloning and functional analysis of multiply spliced mRNA species of human immunodeficiency virus type 1

inferredcites →https://doi.org/10.1128/jvi.64.9.4207-4216.1990openalex-snapshot

Simian immunodeficiency virus displays complex patterns of RNA splicing

inferredcites →https://doi.org/10.1128/jvi.67.11.6365-6378.1993openalex-snapshot

Alternative splicing of human immunodeficiency virus type 1 mRNA modulates viral protein expression, replication, and infectivity

inferredcites →https://doi.org/10.1128/jvi.71.11.8542-8551.1997openalex-snapshot

A naturally arising mutation of a potential silencer of exon splicing in human immunodeficiency virus type 1 induces dominant aberrant splicing and arrests virus production

inferredcites →https://doi.org/10.1128/jvi.75.18.8487-8497.2001openalex-snapshot

RNA Splicing at Human Immunodeficiency Virus Type 1 3′ Splice Site A2 Is Regulated by Binding of hnRNP A/B Proteins to an Exonic Splicing Silencer Element

inferredcites →https://doi.org/10.1128/jvi.78.17.9105-9114.2004openalex-snapshot

Analysis of Human Immunodeficiency Virus Type 1 Transcriptional Elongation in Resting CD4+T Cells In Vivo

inferredcites →https://doi.org/10.1128/jvi.79.16.10478-10486.2005openalex-snapshot

An Exonic Splicing Silencer Downstream of the 3′ Splice Site A2 Is Required for Efficient Human Immunodeficiency Virus Type 1 Replication

inferredcites →https://doi.org/10.1128/mcb.14.6.3960openalex-snapshot

Presence of Negative and Positive cis -Acting RNA Splicing Elements within and Flanking the First tat Coding Exon of Human Immunodeficiency Virus Type 1

inferredcites →https://doi.org/10.1128/mcb.15.8.4606openalex-snapshot

Presence of Exon Splicing Silencers within Human Immunodeficiency Virus Type 1 tat Exon 2 and tat-rev Exon 3: Evidence for Inhibition Mediated by Cellular Factors

inferredcites →https://doi.org/10.1128/mcb.24.24.10505-10514.2004openalex-snapshot

Influence of RNA Secondary Structure on the Pre-mRNA Splicing Process

inferredcites →https://doi.org/10.1186/1742-4690-3-10openalex-snapshot

A suboptimal 5' splice site downstream of HIV-1 splice site A1 is required for unspliced viral mRNA accumulation and efficient virus replication

inferredcites →https://doi.org/10.1186/s12977-015-0205-1openalex-snapshot

Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats

inferredcites →https://doi.org/10.1261/rna.829208openalex-snapshot

Unexpected roles for UPF1 in HIV-1 RNA metabolism and translation

inferredcites →https://doi.org/10.1261/rna.876308openalex-snapshot

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

inferredcites →https://doi.org/10.1371/journal.pone.0012271openalex-snapshot

Apparent Non-Canonical Trans-Splicing Is Generated by Reverse Transcriptase In Vitro

inferredcites →https://doi.org/10.1371/journal.pone.0030574openalex-snapshot

Identification of New Splice Sites Used for Generation of rev Transcripts in Human Immunodeficiency Virus Type 1 Subtype C Primary Isolates

inferredcites →https://doi.org/10.1371/journal.pone.0158525openalex-snapshot

Sequence Analysis of In Vivo-Expressed HIV-1 Spliced RNAs Reveals the Usage of New and Unusual Splice Sites by Viruses of Different Subtypes

inferredcites →https://doi.org/10.1371/journal.ppat.1003294openalex-snapshot

Comparison of SIV and HIV-1 Genomic RNA Structures Reveals Impact of Sequence Evolution on Conserved and Non-Conserved Structural Motifs

inferredcites →https://doi.org/10.2741/3408openalex-snapshot

Role of RNA structure and protein factors in the control of HIV-1 splicing

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Epitranscriptomic Regulation of HIV-1 Gene Expression by m 5C and the Novel m 5C Reader MBD2

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Epitranscriptomic Addition of m 5C to HIV-1 Transcripts Regulates Viral Gene Expression

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Teetering on the Edge

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Epitranscriptomic Addition of m5C to HIV-1 Transcripts Regulates Viral Gene Expression

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Acetylation of Cytidine Residues Boosts HIV-1 Gene Expression by Increasing Viral RNA Stability

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Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for Differential Binding of hnRNP Splicing Auxiliary Factors

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Expression of Herpes Simplex Virus Thymidine Kinase/Ganciclovir by RNA Trans-Splicing Induces Selective Killing of HIV-Producing Cells

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Optimization of a lentivirus-mediated gene therapy targeting HIV-1 RNA to eliminate HIV-1-infected cells

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Behind the scenes of HIV-1 replication: Alternative splicing as the dependency factor on the quiet

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Screening for small molecule inhibitors of HIV-1 Gag expression

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Non-AUG HIV-1 uORF translation elicits specific T cell immune response and regulates viral transcript expression

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HIV-1-encoded circular RNA enhances viral transcription through Tat binding

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Determination of RNA structural diversity and its role in HIV-1 RNA splicing

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Nano-DMS-MaP allows isoform-specific RNA structure determination

inferred← citeshttps://doi.org/10.1038/s44298-025-00105-0openalex-snapshot

Backsplicing of the HIV-1 transcript generates multiple circRNAs to promote viral replication

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HIV-1 infection induces Vif-mediated SUMOylation of host RNA splicing factors important for proper viral RNA splicing

inferred← citeshttps://doi.org/10.1093/nar/gkac516openalex-snapshot

Selective ablation of 3′ RNA ends and processive RTs facilitate direct cDNA sequencing of full-length host cell and viral transcripts

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HIV-2 evades restriction by ZAP through adaptations in the U3 LTR region despite increased CpG levels

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High-resolution HIV-1 m6A epitranscriptome reveals isoform-dependent methylation clusters and unique 2-LTR transcript modifications

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Near normalization of peripheral blood markers in HIV-infected patients on long-term suppressive antiretroviral therapy: a case–control study

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Interferon-α subtype treatment induces the repression of SRSF1 in HIV-1 target cells and affects HIV-1 post integration steps

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The histone methyltransferase SETD2 regulates HIV expression and latency through a post-transcriptional mechanism

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HIV-1 single transcription start site mutants display complementary replication functions that are restored by reversion

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Epitranscriptomic addition of m 6 A regulates HIV-1 RNA stability and alternative splicing

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Insertional activation of STAT3 and LCK by HIV-1 proviruses in T cell lymphomas

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Virion-Associated Vpr Alleviates a Postintegration Block to HIV-1 Infection of Dendritic Cells

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Analysis of Competing HIV-1 Splice Donor Sites Uncovers a Tight Cluster of Splicing Regulatory Elements within Exon 2/2b

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HIV-1 Tat commandeers nuclear export of Rev-viral RNA complex by controlling hnRNPA2-mediated splicing

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Genome-Wide Analysis of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) Binding to HIV-1 RNA Reveals a Key Role for hnRNP H1 in Alternative Viral mRNA Splicing

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Translation of HIV-1 unspliced RNA is regulated by 5′ untranslated region structure

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RNA splicing patterns contribute to burst size variation among HIV-1-infected Jurkat cell clones

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CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent Mechanisms

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HIV-1 single-transcription start-site mutants display complementary replication functions that are restored by reversion

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HIV Silencing and Inducibility Are Heterogeneous and Are Affected by Factors Intrinsic to the Virus

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HIV-1 capsid and viral DNA integration

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Clonally expanded HIV-1 proviruses with 5′-leader defects can give rise to nonsuppressible residual viremia

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Opposing roles of CLK SR kinases in controlling HIV-1 gene expression and latency

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HIV co-opts a cellular antiviral mechanism, activation of stress kinase PKR by its RNA, to enable splicing of rev/tat mRNA

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HIV-1 spliced RNAs display transcription start site bias

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A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance

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Global synonymous mutagenesis identifies cis-acting RNA elements that regulate HIV-1 splicing and replication

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Mutations altering acetylated residues in the CTD of HIV-1 integrase cause defects in proviral transcription at early times after integration of viral DNA

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Expression Level of HIV-1 Vif Can Be Fluctuated by Natural Nucleotide Variations in the vif-Coding and Regulatory SA1D2prox Sequences of the Proviral Genome

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The HIV 5′ Gag Region Displays a Specific Nucleotide Bias Regulating Viral Splicing and Infectivity

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The Antiviral Factor SERINC5 Impairs the Expression of Non-Self-DNA

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Involvement of a Rarely Used Splicing SD2b Site in the Regulation of HIV-1 vif mRNA Production as Revealed by a Growth-Adaptive Mutation

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Host RNA-Binding Proteins as Regulators of HIV-1 Replication

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Additional file 10 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection

inferred← citeshttps://doi.org/10.6084/m9.figshare.12819229openalex-snapshot

Additional file 11 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection

inferred← citeshttps://doi.org/10.6084/m9.figshare.12819232openalex-snapshot

Additional file 12 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection

inferred← citeshttps://doi.org/10.6084/m9.figshare.12819244openalex-snapshot

Additional file 15 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection

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Additional file 5 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection

inferred← citeshttps://doi.org/10.6084/m9.figshare.12819265openalex-snapshot

Additional file 6 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection

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Additional file 8 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection

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Additional file 9 of Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection

inferred← citeshttps://doi.org/10.6084/m9.figshare.20521656openalex-snapshot

Additional file 1 of Opposing roles of CLK SR kinases in controlling HIV-1 gene expression and latency

inferred← citeshttps://doi.org/10.6084/m9.figshare.26568013openalex-snapshot

Additional file 1 of HIV co-opts a cellular antiviral mechanism, activation of stress kinase PKR by its RNA, to enable splicing of rev/tat mRNA

inferred← citeshttps://doi.org/10.70675/40f6be5ez97e5z4043za0cdz0099a87dd935openalex-snapshot

Réplication et séquestration du VIH-1 dans les macrophages

inferred← citeshttps://doi.org/10.70675/5c762198z935ez4a3dza68czd2e7bad030c4openalex-snapshot

Caractérisation biochimique et enzymatique de l’hélicase DDX3 : influence sur la dimérisation de l’ARN génomique du VIH

inferred← citeshttps://doi.org/10.70675/6ce04440z0ddfz4ad2zbbdbzf94bec9b3db0openalex-snapshot

Structural rearrangements of the HIV-1 genomic RNA during maturation of the viral particle

inferred← citeshttps://doi.org/10.70675/ea7dd3c9z2df4z4235z9a72z743f0779fca4openalex-snapshot

Rôles des régulateurs de la marque épitranscriptomique N'6-méthyladénosine dans le contrôle de la réplication virale du VIH-1

inferred← citeshttps://doi.org/10.7554/elife.57246openalex-snapshot

The HIV-1 latent reservoir is largely sensitive to circulating T cells

inferred← citeshttps://doi.org/10.7554/elife.62470openalex-snapshot

Identification of host proteins differentially associated with HIV-1 RNA splice variants

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