Epitranscriptomic addition of m6A regulates HIV-1 RNA stability and alternative splicing

AbstractPrevious work in several laboratories has demonstrated that the epitranscriptomic addition of m6A to viral transcripts promotes the replication and pathogenicity of a wide range of DNA and RNA viruses, yet the underlying mechanisms responsible for this positive effect have remained unclear. It is known that m6A function is largely mediated by cellular m6A binding proteins or readers, yet how m6A readers regulate viral gene expression in general, and HIV-1 gene expression in particular, has been controversial. Here, we confirm that m6A addition indeed regulates HIV-1 RNA expression and demonstrate that this effect is in large part mediated by the the nuclear m6A reader YTHDC1 and the cytoplasmic m6A reader YTHDF2. Both YTHDC1 and YTHDF2 bind to multiple distinct and overlapping sites on the HIV-1 RNA genome, with YTHDC1 recruitment serving to regulate the alternative splicing of HIV-1 RNAs while YTHDF2 binding correlates with increased HIV-1 transcript stability.Author SummaryThis manuscript reports that the expression of mRNAs encoded by the pathogenic human retrovirus HIV-1 is regulated by the methylation of a small number of specific adenosine residues. These in turn recruit a nuclear RNA binding protein, called YTHDC1, which modulates the alternative splicing of HIV-1 transcripts, as well as a cytoplasmic RNA binding protein, called YTHDF2, which stabilizes viral mRNAs. The regulation of HIV-1 gene expression by adenosine methylation is therefore critical for the effective and ordered expression of HIV-1 mRNAs and could represent a novel target for antiviral development.

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Modulation of OPRM1 Alternative Splicing by Morphine and HIV–1 Nef

Journal of Neuroimmune Pharmacology ◽

10.1007/s11481-021-10009-4 ◽

2021 ◽

Author(s):

Martina Donadoni ◽

Wenfei Huang ◽

Shadan S. Yarandi ◽

Tricia H. Burdo ◽

Sulie L. Chang ◽

...

Keyword(s):

Alternative Splicing ◽

Hiv 1

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A Novel Splice Donor Site in thegag-polGene Is Required for HIV-1 RNA Stability

Journal of Biological Chemistry ◽

10.1074/jbc.m513698200 ◽

2006 ◽

Vol 281 (27) ◽

pp. 18644-18651 ◽

Cited By ~ 20

Author(s):

Martin Lützelberger ◽

Line S. Reinert ◽

Atze T. Das ◽

Ben Berkhout ◽

Jørgen Kjems

Keyword(s):

Donor Site ◽

Rna Stability ◽

Splice Donor Site ◽

Splice Donor ◽

Hiv 1

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Polymorphisms and Splice Variants Influence the Antiretroviral Activity of Human APOBEC3H

Journal of Virology ◽

10.1128/jvi.01665-08 ◽

2008 ◽

Vol 83 (1) ◽

pp. 295-303 ◽

Cited By ~ 117

Author(s):

Ariana Harari ◽

Marcel Ooms ◽

Lubbertus C. F. Mulder ◽

Viviana Simon

Keyword(s):

Alternative Splicing ◽

Mononuclear Cells ◽

Splice Variants ◽

Genomic Variation ◽

Endogenous Retroviruses ◽

Site Directed Mutagenesis ◽

Wide Range ◽

The Impact ◽

Hiv 1 ◽

Antiretroviral Activity

ABSTRACT Human APOBEC3H belongs to the APOBEC3 family of cytidine deaminases that potently inhibit exogenous and endogenous retroviruses. The impact of single nucleotide polymorphisms (SNP) and alternative splicing on the antiretroviral activity of human APOBEC3H is currently unknown. In this study, we show that APOBEC3H transcripts derived from human peripheral blood mononuclear cells are polymorphic in sequence and subject to alternative splicing. We found that APOBEC3H variants encoding a SNP cluster (G105R, K121D and E178D, hapII-RDD) restricted human immunodeficiency virus type 1 (HIV-1) more efficiently than wild-type APOBEC3H (hapI-GKE). All APOBEC3H variants tested were resistant to HIV-1 Vif, the viral protein that efficiently counteracts APOBEC3G/3F activity. Alternative splicing of APOBEC3H was common and resulted in variants with distinct C-terminal regions and variable antiretroviral activities. Splice variants of hapI-GKE displayed a wide range of antiviral activities, whereas similar splicing events in hapII-RDD resulted in proteins that uniformly and efficiently restricted viral infectivity (>20-fold). Site-directed mutagenesis identified G105R in hapI-GKE and D121K in hapII-RDD as critical substitutions leading to an average additional 10-fold increase in antiviral activity. APOBEC3H variants were catalytically active and, similarly to APOBEC3F, favored a GA dinucleotide context. HIV-1 mutagenesis as a mode of action for APOBEC3H is suggested by the decrease of restriction observed with a cytidine deaminase domain mutant and the inverse correlation between G-to-A mutations and infectivity. Thus, the anti-HIV activity of APOBEC3H seems to be regulated by a combination of genomic variation and alternative splicing. Since prevalence of hapII-RDD is high in populations of African descent, these findings raise the possibility that some individuals may harbor effective as well as HIV-1 Vif-resistant intracellular antiviral defense mechanisms.

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Acetylation of cytidine residues boosts HIV-1 gene expression by increasing viral RNA stability

10.1101/2020.01.31.925578 ◽

2020 ◽

Author(s):

Kevin Tsai ◽

Ananda Ayyappan Jaguva Vasudevan ◽

Cecilia Martinez Campos ◽

Ann Emery ◽

Ronald Swanstrom ◽

...

Keyword(s):

Gene Expression ◽

Rna Stability ◽

Antiviral Drug ◽

Viral Gene Expression ◽

Mrna Translation ◽

Viral Gene ◽

Viral Mrnas ◽

Cellular Target ◽

Covalent Modifications ◽

Hiv 1

AbstractCovalent modifications added to individual nucleotides on mRNAs, called epitranscriptomic modifications, have recently emerged as key regulators of both cellular and viral mRNA function1,2 and RNA methylation has now been shown to enhance the replication of human immunodeficiency virus 1 (HIV-1) and several other viruses3–11. Recently, acetylation of the N4 position of cytidine (ac4C) was reported to boost cellular mRNA function by increasing mRNA translation and stability12. We therefore hypothesized that ac4C and N-acetyltransferase 10 (NAT10), the cellular enzyme that adds ac4C to RNAs, might also have been subverted by HIV-1 to increase viral gene expression. We now confirm that HIV-1 transcripts are indeed modified by addition of ac4C at multiple discreet sites and demonstrate that silent mutagenesis of a subset of these ac4C addition sites inhibits HIV-1 gene expression in cis. Moreover, reduced expression of NAT10, and the concomitant decrease in the level of ac4C on viral RNAs, inhibits HIV-1 replication by reducing HIV-1 RNA stability. Interestingly Remodelin, a previously reported inhibitor of NAT10 function13,14, also inhibits HIV-1 replication without affecting cell viability, thus raising the possibility that the addition of ac4C to viral mRNAs might emerge as a novel cellular target for antiviral drug development.

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Acetylation of cytidine residues boosts HIV-1 gene expression by increasing viral RNA stability

10.26226/morressier.5ebd45acffea6f735881b035 ◽

2020 ◽

Author(s):

Kevin Tsai

Keyword(s):

Gene Expression ◽

Rna Stability ◽

Viral Rna ◽

Hiv 1

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An Alu Element Insertion in Intron 1 Results in Aberrant Alternative Splicing of APOBEC3G Pre-mRNA in Northern Pig-Tailed Macaques (Macaca leonina) That May Reduce APOBEC3G-Mediated Hypermutation Pressure on HIV-1

Journal of Virology ◽

10.1128/jvi.01722-19 ◽

2019 ◽

Vol 94 (4) ◽

Author(s):

Xiao-Liang Zhang ◽

Meng-Ting Luo ◽

Jia-Hao Song ◽

Wei Pang ◽

Yong-Tang Zheng

Keyword(s):

Alternative Splicing ◽

Animal Models ◽

Family Members ◽

Element Insertion ◽

Intron 1 ◽

Splicing Pattern ◽

Alu Element ◽

Aids Therapy ◽

Apobec3 Family ◽

Hiv 1

ABSTRACT APOBEC3 family members, particularly APOBEC3F and APOBEC3G, inhibit the replication and spread of various retroviruses by inducing hypermutation in newly synthesized viral DNA. Viral hypermutation by APOBEC3 is associated with viral evolution, viral transmission, and disease progression. In recent years, increasing attention has been paid to targeting APOBEC3G for AIDS therapy. Thus, a controllable model system using species such as macaques, which provide a relatively ideal in vivo system, is needed for the study of APOBEC3-related issues. To appropriately utilize this animal model for biomedical research, important differences between human and macaque APOBEC3s must be considered. In this study, we found that the ratio of APOBEC3G-mediated/APOBEC3-mediated HIV-1 hypermutation footprints was much lower in peripheral blood mononuclear cells (PBMCs) from northern pig-tailed macaques than in PBMCs from humans. Next, we identified a novel and conserved APOBEC3G pre-mRNA alternative splicing pattern in macaques, which differed from that in humans and resulted from an Alu element insertion into macaque APOBEC3G gene intron 1. This alternative splicing pattern generating an aberrant APOBEC3G mRNA isoform may significantly dilute full-length APOBEC3G and reduce APOBEC3G-mediated hypermutation pressure on HIV-1 in northern pig-tailed macaques, which was supported by the elimination of other possibilities accounting for this hypermutation difference between the two hosts. IMPORTANCE APOBEC3 family members, particularly APOBEC3F and APOBEC3G, are important cellular antiviral factors. Recently, more attention has been paid to targeting APOBEC3G for AIDS therapy. To appropriately utilize macaque animal models for the study of APOBEC3-related issues, it is important that the differences between human and macaque APOBEC3s are clarified. In this study, we identified a novel and conserved APOBEC3G pre-mRNA alternative splicing pattern in macaques, which differed from that in humans and which may reduce the APOBEC3G-mediated hypermutation pressure on HIV-1 in northern pig-tailed macaques (NPMs). Our work provides important information for the proper application of macaque animal models for APOBEC3-related issues in AIDS research and a better understanding of the biological functions of APOBEC3 proteins.

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Alternative splicing: regulation of HIV-1 multiplication as a target for therapeutic action

FEBS Journal ◽

10.1111/j.1742-4658.2009.07522.x ◽

2010 ◽

Vol 277 (4) ◽

pp. 867-876 ◽

Cited By ~ 59

Author(s):

Jamal Tazi ◽

Nadia Bakkour ◽

Virginie Marchand ◽

Lilia Ayadi ◽

Amina Aboufirassi ◽

...

Keyword(s):

Alternative Splicing ◽

Splicing Regulation ◽

Therapeutic Action ◽

Hiv 1

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Functional replacement of the R region of simian immunodeficiency virus-based vectors by heterologous elements

Journal of General Virology ◽

10.1099/vir.0.81883-0 ◽

2006 ◽

Vol 87 (8) ◽

pp. 2297-2307 ◽

Cited By ~ 6

Author(s):

Sabine Brandt ◽

Thomas Grunwald ◽

Susann Lucke ◽

Alexander Stang ◽

Klaus Überla

Keyword(s):

Simian Immunodeficiency Virus ◽

Rna Stability ◽

Vector Particle ◽

Cytoplasmic Rna ◽

Immunodeficiency Virus ◽

R Region ◽

Cellular Sequence ◽

Murine Sarcoma Virus ◽

Steady State Levels ◽

Hiv 1

Substitution of lentiviral cis-acting elements by heterologous sequences might allow the safety of lentiviral vectors to be enhanced by reducing the risk of homologous recombination and vector mobilization. Therefore, a substitution and deletion analysis of the R region of simian immunodeficiency virus (SIV)-based vectors was performed and the effect of the modifications on packaging and transfer by SIV and human immunodeficiency virus type 1 (HIV-1) particles was analysed. Deletion of the first 7 nt of R reduced vector titres by 10- to 20-fold, whilst deletion of the entire R region led to vector titres that were 1500-fold lower. Replacement of the R region of SIV-based vectors by HIV-1 or Moloney murine sarcoma virus R regions partially restored vector titres. A non-retroviral cellular sequence was also functional, although to a lesser extent. In the absence of tat, modification of the R region had only minor effects on cytoplasmic RNA stability, steady-state levels of vector RNA and packaging, consistent with the known primary function of R during reverse transcription. Although the SIV R region of SIV-based vectors could be replaced functionally by heterologous sequences, the same modifications of R led to a severe replication defect in the context of a replication-competent SIV. As SIV-based vectors containing the HIV-1 R region were transferred less efficiently by HIV-1 particles than wild-type SIV vectors, a match between R and cis-acting elements of the vector construct seems to be more important than a match between R and the Gag or Pol proteins of the vector particle.

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