Cited by 42RNA modifications and cancerHIV Research and TreatmentRNA regulation and disease

Epitranscriptomic regulation of HIV-1 full-length RNA packaging

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Pereira-Montecinos, Camila, Toro-Ascuy, Daniela, Ananías-Sáez, Catarina, Gaete-Argel, Aracelly, Rojas-Fuentes, Cecilia, Riquelme-Barrios, Sebastián, Rojas-Araya, Bárbara, García-de-Gracia, Francisco +5 more·2022·Nucleic Acids Research

Abstract

During retroviral replication, the full-length RNA serves both as mRNA and genomic RNA. However, the mechanisms by which the HIV-1 Gag protein selects the two RNA molecules that will be packaged into nascent virions remain poorly understood. Here, we demonstrate that deposition of N6-methyladenosine (m6A) regulates full-length RNA packaging. While m6A deposition by METTL3/METTL14 onto the full-length RNA was associated with increased Gag synthesis and reduced packaging, FTO-mediated demethylation promoted the incorporation of the full-length RNA into viral particles. Interestingly, HIV-1 Gag associates with the RNA demethylase FTO in the nucleus and contributes to full-length RNA demethylation. We further identified two highly conserved adenosines within the 5'-UTR that have a crucial functional role in m6A methylation and packaging of the full-length RNA. Together, our data propose a novel epitranscriptomic mechanism allowing the selection of the HIV-1 full-length RNA molecules that will be used as viral genomes.

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  1. [1]Karn J., Stoltzfus C.M. Transcriptional and posttranscriptional regulation of HIV-1 gene expression. Cold Spring Harb. Perspect. Med. 2012; 2: a006916. 22355797 PMC3281586
  2. [2]Butsch M., Boris-lawrie K. Destiny of unspliced retroviral RNA: ribosome and/or virion. J. Virol. 2002; 76: 3089– 3094. 11884533 PMC136024
  3. [3]Mailler E., Bernacchi S., Marquet R., Paillart J.C., Vivet-Boudou V., Smyth R.P. The life-cycle of the HIV-1 gag–RNA complex. Viruses. 2016; 8: 248. PMC5035962 27626439
  4. [4]Levin J.G., Grimley P.M., Ramseur J.M., Berezesky I.K. Deficiency of 60 to 70S RNA in murine leukemia virus particles assembled in cells treated with actinomycin D. J. Virol. 1974; 14: 152– 161. 4134468 PMC355489
  5. [5]Levin J.G., Rosenak M.J. Synthesis of murine leukemia virus proteins associated with virions assembled in actinomycin d treated cells: evidence for persistence of viral messenger RNA. Proc. Natl. Acad. Sci. U.S.A. 1976; 73: 1154– 1158. 57617 PMC430219
  6. [6]Dorman N., Lever A. Comparison of viral genomic RNA sorting mechanisms in human immunodeficiency virus type 1 (HIV-1), HIV-2, and moloney murine leukemia virus. J. Virol. 2000; 74: 11413– 11417. 11070043 PMC113248
  7. [7]Chen J., Liu Y., Wu B., Nikolaitchik O.A., Mohan P.R., Chen J., Pathak V.K., Hu W.S. Visualizing the translation and packaging of HIV-1 full-length RNA. Proc. Natl. Acad. Sci. U.S.A. 2020; 117: 6154– 6155. PMC7084099 32132202
  8. [8]Laughrea M., Jetté L., Mak J., Kleiman L., Liang C., Wainberg M.A. Mutations in the kissing-loop hairpin of human immunodeficiency virus type 1 reduce viral infectivity as well as genomic RNA packaging and dimerization. J. Virol. 1997; 71: 3397– 3406. 9094609 PMC191484
  9. [9]Chen J., Rahman S.A., Nikolaitchik O.A., Grunwald D., Sardo L., Burdick R.C., Plisov S., Liang E., Tai S., Pathak V.K. et al. HIV-1 RNA genome dimerizes on the plasma membrane in the presence of gag protein. Proc. Natl. Acad. Sci. U.S.A. 2016; 113: E201– E208. 26712001 PMC4720333
  10. [10]Clever J.L., Parslow T.G. Mutant human immunodeficiency virus type 1 genomes with defects in RNA dimerization or encapsidation. J. Virol. 1997; 71: 3407– 3414. 9094610 PMC191485
  11. [11]Ferrer M., Clerté C., Chamontin C., Basyuk E., Lainé S., Hottin J., Bertrand E., Margeat E., Mougel M. Imaging HIV-1 RNA dimerization in cells by multicolor super-resolution and fluctuation microscopies. Nucleic Acids Res. 2016; 44: 7922– 7934. 27280976 PMC5027490
  12. [12]Huthoff H., Berkhout B. Two alternating structures of the HIV-1 leader RNA. RNA. 2001; 7: 143– 157. 11214176 PMC1370064
  13. [13]Berkhout B., Ooms M., Beerens N., Huthoff H., Southern E., Verhoef K. In vitro evidence that the untranslated leader of the HIV-1 genome is an RNA checkpoint that regulates multiple functions through conformational changes. J. Biol. Chem. 2002; 277: 19967– 19975. 11896057
  14. [14]Abbink T.E.M., Berkhout B. A novel long distance base-pairing interaction in human immunodeficiency virus type 1 rna occludes the gag start codon. J. Biol. Chem. 2003; 278: 11601– 11611. 12458192
  15. [15]Keane S.C., Heng X., Lu K., Kharytonchyk S., Ramakrishnan V., Carter G., Barton S., Hosic A., Florwick A., Santos J. et al. Structure of the HIV-1 RNA packaging signal. Science. 2015; 348: 917– 921. 25999508 PMC4492308
  16. [16]Kuzembayeva M., Dilley K., Sardo L., Hu W.S. Life of psi: how full-length HIV-1 RNAs become packaged genomes in the viral particles. Virology. 2014; 454–455: 362– 370. PMC6258065 24530126
  17. [17]Watts J.M., Dang K.K., Gorelick R.J., Leonard C.W., Bess J.W., Swanstrom R., Burch C.L., Weeks K.M. Architecture and secondary structure of an entire HIV-1 RNA genome. Nature. 2009; 460: 711– 716. 19661910 PMC2724670
  18. [18]El-Wahab E.W.A., Smyth R.P., Mailler E., Bernacchi S., Vivet-Boudou V., Hijnen M., Jossinet F., Mak J., Paillart J.C., Marquet R. Specific recognition of the HIV-1 genomic RNA by the gag precursor. Nat. Commun. 2014; 5: 4304. 24986025
  19. [19]Siegfried N.A., Busan S., Rice G.M., Nelson J.A.E., Weeks K.M. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat. Methods. 2014; 11: 959– 965. 25028896 PMC4259394
  20. [20]Paillart J.C., Dettenhofer M., Yu X.F., Ehresmann C., Ehresmann B., Marquet R. First snapshots of the HIV-1 RNA structure in infected cells and in virions. J. Biol. Chem. 2004; 279: 48397– 48403. 15355993
  21. [21]Abbink T.E.M., Ooms M., Haasnoot P.C.J., Berkhout B. The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation. Biochemistry. 2005; 44: 9058– 9066. 15966729
  22. [22]Boeras I., Seufzer B., Brady S., Rendahl A., Heng X., Boris-Lawrie K. The basal translation rate of authentic HIV-1 RNA is regulated by 5′UTR nt-pairings at junction of r and u5. Sci. Rep. 2017; 7: 6902. 28761163 PMC5537239
  23. [23]Lichinchi G., Gao S., Saletore Y., Gonzalez G.M., Bansal V., Wang Y., Mason C.E., Rana T.M. Dynamics of the human and viral m 6 a RNA methylomes during HIV-1 infection of t cells. Nat. Microbiol. 2016; 1: 16011. 27572442 PMC6053355
  24. [24]Kennedy E.M., Bogerd H.P., Kornepati A.V.R., Kang D., Ghoshal D., Marshall J.B., Poling B.C., Tsai K., Gokhale N.S., Horner S.M. et al. Posttranscriptional m6A editing of HIV-1 mRNAs enhances viral gene expression. Cell Host Microbe. 2016; 19: 675– 685. 27117054 PMC4867121
  25. [25]Tirumuru N., Zhao B.S., Lu W., Lu Z. N6 -methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 gag protein expression. elife. 2016; 5: e15528. 27371828 PMC4961459
  26. [26]Lu W., Tirumuru N., Gelais C.S., Koneru P.C., Liu C., Kvaratskhelia M., He C., Wu L. N6-Methyladenosine– binding proteins suppress HIV-1 infectivity and viral production. J. Biol. Chem. 2018; 293: 12992– 13005. 29976753 PMC6109920
  27. [27]Toro-Ascuy D., Rojas-Araya B., García-de-Gracia F., Rojas-Fuentes C., Pereira-Montecinos C., Gaete-Argel A., Valiente-Echeverría F., Ohlmann T., Soto-Rifo R. A Rev–CBP80–eIF4AI complex drives gag synthesis from the HIV-1 unspliced mRNA. Nucleic Acids Res. 2018; 46: 11539– 11552. 30239828 PMC6265489
  28. [28]Mangeot P.-E., Nègre D., Dubois B., Winter A.J., Leissner P., Mehtali M., Kaiserlian D., Cosset F.-L., Darlix J.-L. Development of minimal lentivirus vectors derived from simian immunodeficiency virus (SIVmac251) and their use for gene transfer into human dendritic cells. J. Virol. 2000; 74: 8307– 8315. 10954529 PMC116340
  29. [29]Liu J., Yue Y., Han D., Wang X., Fu Y., Zhang L., Jia G., Yu M., Lu Z., Deng X. et al. A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat. Chem. Biol. 2014; 10: 93– 95. 24316715 PMC3911877
  30. [30]Zheng G., Dahl J.A., Niu Y., Fedorcsak P., Huang C.M., Li C.J., Vågbø C.B., Shi Y., Wang W.L., Song S.H. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell. 2013; 49: 18– 29. 23177736 PMC3646334
  31. [31]Jia G., Fu Y., Zhao X., Dai Q., Zheng G., Yang Y., Yi C., Lindahl T., Pan T., Yang Y. et al. N 6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 2011; 7: 6– 9. PMC3218240 22002720
  32. [32]Soto-Rifo R., Rubilar P.S., Ohlmann T. The DEAD-box helicase DDX3 substitutes for the cap-binding protein eIF4E to promote compartmentalized translation initiation of the HIV-1 genomic RNA. Nucleic Acids Res. 2013; 41: 6286– 6299. 23630313 PMC3695493
  33. [33]Schwartz S., Felber B.K., Pavlakis G.N. Distinct RNA sequences in the gag region of human immunodeficiency virus type 1 decrease RNA stability and inhibit expression in the absence of rev protein. J. Virol. 1992; 66: 150– 159. 1727477 PMC238270
  34. [34]Fröhlich A., Rojas-Araya B., Pereira-Montecinos C., Dellarossa A., Toro-Ascuy D., Prades-Pérez Y., García-de-Gracia F., Garcés-Alday A., Rubilar P.S., Valiente-Echeverría F. et al. DEAD-box RNA helicase DDX3 connects CRM1-dependent nuclear export and translation of the HIV-1 unspliced mRNA through its N-terminal domain. Biochim. Biophys. Acta - Gene Regul. Mech. 2016; 1859: 719– 730. 27012366
  35. [35]Feng J., Liu T., Zhang Y. Using MACS to identify peaks from chip-seq data. Curr. Protoc. Bioinformatics. 2011; Chapter 2: Unit 2.14. PMC3120977 21633945
  36. [36]Zhou Y., Zeng P., Li Y.H., Zhang Z., Cui Q. SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features. Nucleic Acids Res. 2016; 44: e91. 26896799 PMC4889921
  37. [37]García-de-Gracia F., Gaete-Argel A., Riquelme-Barrios S., Pereira-Montecinos C., Rojas-Araya B., Aguilera Paulina, Oyarzún-Arrau A., Rojas-Fuentes C., Acevedo M.L, Chnaiderman J., Valiente-Echeverría F., Toro-Ascuy D., Soto-Rifo R. CBP80/20-dependent translation initiation factor (CTIF) inhibits HIV-1 Gag synthesis by targeting the function of the viral protein Rev. RNA Biol. 2021; 18: 745– 758. 33103564 PMC8078705
  38. [38]Briggs J.A.G., Simon M.N., Gross I., Kräusslich H.G., Fuller S.D., Vogt V.M., Johnson M.C. The stoichiometry of gag protein in HIV-1. Nat. Struct. Mol. Biol. 2004; 11: 672– 675. 15208690
  39. [39]Onafuwa-Nuga A.A., Telesnitsky A., King S.R. 7SL RNA, but not the 54-kd signal recognition particle protein, is an abundant component of both infectious HIV-1 and minimal virus-like particles. RNA. 2006; 12: 542– 546. 16489186 PMC1421090
  40. [40]Houzet L., Paillart J.C., Smagulova F., Maurel S., Morichaud Z., Marquet R., Mougel M. HIV controls the selective packaging of genomic, spliced viral and cellular RNAs into virions through different mechanisms. Nucleic Acids Res. 2007; 35: 2695– 2704. 17426127 PMC1885669
  41. [41]Kharytonchyk S., Monti S., Smaldino P.J., Van V., Bolden N.C., Brown J.D., Russo E., Swanson C., Shuey A., Telesnitsky A. et al. Transcriptional start site heterogeneity modulates the structure and function of the HIV-1 genome. Proc. Natl. Acad. Sci. U.S.A. 2016; 113: 13378– 13383. 27834211 PMC5127319
  42. [42]Masuda T., Sato Y., Huang Y.L., Koi S., Takahata T., Hasegawa A., Kawai G., Kannagi M. Fate of HIV-1 cDNA intermediates during reverse transcription is dictated by transcription initiation site of virus genomic RNA. Sci. Rep. 2015; 5: 17680. 26631448 PMC4668388
  43. [43]Brown J.D., Kharytonchyk S., Chaudry I., Iyer A.S., Carter H., Becker G., Desai Y., Glang L., Choi S.H., Singh K. et al. Structural basis for transcriptional start site control of HIV-1 RNA fate. Science. 2020; 368: 413– 417. 32327595 PMC7351118
  44. [44]Keane S.C., Van V., Frank H.M., Sciandra C.A., McCowin S., Santos J., Heng X., Summers M.F. NMR detection of intermolecular interaction sites in the dimeric 5′-leader of the HIV-1 genome. Proc. Natl. Acad. Sci. U.S.A. 2016; 113: 13033– 13038. 27791166 PMC5135362
  45. [45]Darnell R.R., Shengdong K.E., Darnell J.E. Pre-mRNA processing includes N6 methylation of adenosine residues that are retained in mRNA exons and the fallacy of “RNA epigenetics”. RNA. 2018; 24: 262– 267. 29222117 PMC5824346
  46. [46]Lochmann T.L., Bann D. V., Ryan E.P., Beyer A.R., Mao A., Cochrane A., Parent L.J. NC-mediated nucleolar localization of retroviral gag proteins. Virus Res. 2013; 171: 304– 318. 23036987 PMC3578147
  47. [47]Maldonado R.J.K., Rice B., Chen E.C., Tuffy K.M., Chiari E.F., Fahrbach K.M., Hope T.J., Parent L.J. Visualizing association of the retroviral gag protein with unspliced viral RNA in the nucleus. MBio. 2020; 11: e00524-20. 32265329 PMC7157774
  48. [48]Yu K.L., Lee S.H., Lee E.S., You J.C. HIV-1 nucleocapsid protein localizes efficiently to the nucleus and nucleolus. Virology. 2016; 492: 204– 212. 26967976
  49. [49]Tuffy K.M., Maldonado R.J.K., Chang J., Rosenfeld P., Cochrane A., Parent L.J. HIV-1 gag forms ribonucleoprotein complexes with unspliced viral RNA at transcription sites. Viruses. 2020; 12: 1281. PMC7696413 33182496
  50. [50]Huang Y., Yan J., Li Q., Li J., Gong S., Zhou H., Gan J., Jiang H., Jia G.F., Luo C. et al. Meclofenamic acid selectively inhibits FTO demethylation of m6A over ALKBH5. Nucleic Acids Res. 2015; 43: 373– 384. 25452335 PMC4288171
  51. [51]Didierlaurent L., Racine P.J., Houzet L., Chamontin C., Berkhout B., Mougel M. Role of HIV-1 RNA and protein determinants for the selective packaging of spliced and unspliced viral RNA and host U6 and 7SL RNA in virus particles. Nucleic Acids Res. 2011; 39: 8915– 8927. 21791531 PMC3203606
  52. [52]Riquelme-Barrios S., Pereira-Montecinos C., Valiente-Echeverría F., Soto-Rifo R. Emerging roles of N6-methyladenosine on HIV-1 RNA metabolism and viral replication. Front. Microbiol. 2018; 9: 576. 29643844 PMC5882793
  53. [53]Kutluay S.B., Zang T., Blanco-Melo D., Powell C., Jannain D., Errando M., Bieniasz P.D. Global changes in the RNA binding specificity of HIV-1 gag regulate virion genesis. Cell. 2014; 159: 1096– 1109. 25416948 PMC4247003
  54. [54]Wilkinson K.A., Gorelick R.J., Vasa S.M., Guex N., Rein A., Mathews D.H., Giddings M.C., Weeks K.M. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol. 2008; 6: 883– 899. PMC2689691 18447581
  55. [55]Mougel M., Akkawi C., Chamontin C., Feuillard J., Pessel-Vivares L., Socol M., Laine S. NXF1 and CRM1 nuclear export pathways orchestrate nuclear export, translation and packaging of murine leukaemia retrovirus unspliced RNA. RNA Biol. 2020; 4: 528– 538. PMC7237160 31918596
  56. [56]Toro-Ascuy D., Rojas-Araya B., García-de-Gracia F., Rojas-Fuentes C., Pereira-Montecinos C., Gaete-Argel A., Valiente-Echeverría F., Ohlmann T., Soto-Rifo R. A Rev–CBP80–eIF4AI complex drives gag synthesis from the HIV-1 unspliced mRNA. Nucleic Acids Res. 2018; 46: 11539– 11552. 30239828 PMC6265489
  57. [57]Blissenbach M., Grewe B., Hoffmann B., Brandt S., Überla K. Nuclear RNA export and packaging functions of HIV-1 rev revisited. J. Virol. 2010; 84: 6598– 6604. 20427541 PMC2903257
  58. [58]Flynn J.A., Telesnitsky A. Two distinct moloney murine leukemia virus RNAs produced from a single locus dimerize at random. Virology. 2006; 344: 391– 400. 16216294 PMC1351320
  59. [59]Maurel S., Mougel M. Murine leukemia virus RNA dimerization is coupled to transcription and splicing processes. Retrovirology. 2010; 7: 64. 20687923 PMC2925334
  60. [60]Liu N., Zhou K.I., Parisien M., Dai Q., Diatchenko L., Pan T. N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein. Nucleic Acids Res. 2017; 45: 6051– 6063. 28334903 PMC5449601
  61. [61]Gokhale N.S., McIntyre A.B.R., McFadden M.J., Roder A.E., Kennedy E.M., Gandara J.A., Hopcraft S.E., Quicke K.M., Vazquez C., Willer J. et al. N6-Methyladenosine in flaviviridae viral RNA genomes regulates infection. Cell Host Microbe. 2016; 20: 654– 665. 27773535 PMC5123813
  62. [62]Mauer J., Jaffrey S.R. FTO, m 6 a m, and the hypothesis of reversible epitranscriptomic mRNA modifications. FEBS Lett. 2018; 592: 2012– 2022. 29754392
  63. [63]Huang Y., Su R., Sheng Y., Dong L., Dong Z., Xu H., Ni T., Zhang Z.S., Zhang T., Li C. et al. Small-Molecule targeting of oncogenic FTO demethylase in acute myeloid leukemia. Cancer Cell. 2019; 35: 677– 691. 30991027 PMC6812656

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Authors
Pereira-Montecinos, C., Toro-Ascuy, D., Ananías-Sáez, C., Gaete-Argel, A., Rojas-Fuentes, C., Riquelme-Barrios, S., Rojas-Araya, B., García-de-Gracia, F., Aguilera-Cortés, P., Chnaiderman, J., Acevedo, M. L., Valiente-Echeverría, F., & Soto-Rifo, R.
Affiliations
  • University of Chile (CL)
  • Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
  • Millennium Institute on Immunology and Immunotherapy (CL)
Venue
Nucleic Acids Research
Published
2022-02-08
Volume
50
Issue
4
Pages
2302-2318
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
OpenAlex
W4210307847
Cited by
42
References
0
Citations by year
2026: 5 · 2025: 13 · 2024: 14 · 2023: 5 · 2022: 5
FWCI
3.02
Type
journal article
Language
en
Open access
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Universidad de Chile (submittedVersion, cc-by-nc-nd)
Funders
  • FONDECYT (1160176, 1190156, 1180798, 1211547, 11180621)
  • ANID - ICM (ICN2021_045)
  • CONICYT
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
  • Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords
HIV-1, N6-methyladenosine, epitranscriptomics, Gag protein, RNA demethylation, 5' untranslated region, retroviral replication, RNA methylation
MeSH terms
Adenosine, Methylation, RNA, Viral, Virion, HIV-1, Gene Products, gag, 5' Untranslated Regions

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