Retroviruses are among the most extensively studied viral families, both historically and in contemporary research. They are primarily investigated in the fields of viral oncogenesis, reverse transcription mechanisms, and other infection-specific aspects. These include the integration of endogenous retroviruses (ERVs) into host genomes, a process widely utilized in genetic engineering, and the ongoing search for HIV/AIDS treatment. G-quadruplexes (G4) have emerged as potential therapeutic targets in antiviral therapy and have been identified in important regulatory regions of viral genomes. In this study, we examine the presence of potential G-quadruplex-forming sequences (PQS) across all currently available unique retroviral genomes. Given that these retroviral genomes typically consist of single-stranded RNA (ssRNA) molecules, we also investigated whether the localization of PQSs is strand-dependent. This is particularly relevant since antisense transcripts have been detected in HIV, and ERV integration into the host genome involves reverse transcription from genomic positive strand ssRNA to double-stranded DNA (dsDNA), implicating both strands in this process. We show that in most mammalian retroviruses, including human retroviruses, PQSs are significantly more prevalent on the negative (antisense) strand, with some notable exceptions such as HIV-1. In sharp contrast, avian retroviruses exhibit a higher prevalence of PQSs on the positive (sense) strand.

Faculty of Chemistry Brno University of Technology Purkyňova 118 Brno 61200 Czech Republic

Faculty of Science National Centre for Biomolecular Research Masaryk University Kamenice 5 Brno 625 00 Czech Republic

Institute of Biophysics Czech Academy of Sciences Královopolská 135 Brno 612 65 Czech Republic

Laboratoire d'Optique et Biosciences Ecole Polytechnique CNRS INSERM Institut Polytechnique de Paris Palaiseau 91120 France

Zobrazit více v PubMed

Gellert, M., Lipsett, M. N. & Davies, D. R. HELIX FORMATION BY GUANYLIC ACID. Proc. Natl. Acad. Sci. U S A. 48, 2013–2018 (1962). PubMed PMC

Bochman, M. L., Paeschke, K. & Zakian, V. A. DNA secondary structures: stability and function of G-quadruplex structures. Nat. Rev. Genet.13, 770–780 (2012). PubMed PMC

Cantara, A. et al. G-quadruplexes in helminth parasites. Nucleic Acids Res.50, 2719–2735 (2022). PubMed PMC

Brázda, V., Valková, N., Dobrovolná, M. & Mergny, J. L. Abundance of G-Quadruplex forming sequences in the Hepatitis Delta Virus genomes. ACS Omega. 9, 4096–4101 (2024). PubMed PMC

Brázda, V. et al. G-Quadruplexes in the Archaea Domain. Biomolecules10, 1349 (2020). PubMed PMC

Wu, F. et al. Genome-wide analysis of DNA G-quadruplex motifs across 37 species provides insights into G4 evolution. Commun. Biol.4, 1–11 (2021). PubMed PMC

Goswami, P. et al. SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci. Brief. Bioinform. 22, 1338–1345 (2020). PubMed PMC

Kharel, P., Becker, G., Tsvetkov, V. & Ivanov, P. Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back. Nucleic Acids Res.48, 12534 (2020). PubMed PMC

Ding, Y., Fleming, A. M. & Burrows, C. J. Case studies on potential G-quadruplex-forming sequences from the bacterial orders Deinococcales and Thermales derived from a survey of published genomes. Sci. Rep.8, 15679 (2018). PubMed PMC

Falabella, M. et al. G-quadruplex dynamics contribute to regulation of mitochondrial gene expression. Sci. Rep.9, 5605 (2019). PubMed PMC

Brázda, V., Bohálová, N. & Bowater, R. P. New telomere to telomere assembly of human chromosome 8 reveals a previous underestimation of G-quadruplex forming sequences and inverted repeats. Gene810, 146058 (2022). PubMed

Bohálová, N., Mergny, J. L. & Brázda, V. Novel G-quadruplex prone sequences emerge in the complete assembly of the human X chromosome. Biochimie191, 87–90 (2021). PubMed

Spiegel, J., Adhikari, S. & Balasubramanian, S. The structure and function of DNA G-Quadruplexes. Trends Chem.2, 123–136 (2020). PubMed PMC

Gehring, K., Leroy, J. L. & Guéron, M. A tetrameric DNA structure with protonated cytosine-cytosine base pairs. Nature363, 561–565 (1993). PubMed

Ruggiero, E., Zanin, I., Terreri, M. & Richter, S. N. G-Quadruplex Targeting in the fight against viruses: an update. Int. J. Mol. Sci.22, 10984 (2021). PubMed PMC

Brázda, V., Hároníková, L., Liao, J. & Fojta, M. DNA and RNA quadruplex-binding proteins. Int. J. Mol. Sci.15, 17493–17517 (2014). PubMed PMC

Bourdon, S. et al. QUADRatlas: the RNA G-quadruplex and RG4-binding proteins database. Nucleic Acids Res.51, D240–D247 (2023). PubMed PMC

Zareie, A. R., Dabral, P. & Verma, S. C. G-Quadruplexes in the regulation of viral gene expressions and their impacts on Controlling infection. Pathogens13, 60 (2024). PubMed PMC

Ruggiero, E. & Richter, S. N. Chapter Four - Viral G-quadruplexes: New frontiers in virus pathogenesis and antiviral therapy. in Annual Reports in Medicinal Chemistry (ed. Neidle, S.) vol. 54 101–131Academic Press, (2020). PubMed PMC

Abiri, A. et al. Unlocking G-Quadruplexes as antiviral targets. Pharmacol. Rev.73, 897–923 (2021). PubMed

Ruggiero, E. & Richter, S. N. G-Quadruplexes in Human viruses: a Promising Route to innovative antiviral therapies. in Handbook of Chemical Biology of Nucleic Acids (ed. Sugimoto, N.) 1–29 (Springer Nature, Singapore, doi:10.1007/978-981-16-1313-5_81-1. (2022).

Cian, A. D. & Mergny, J. L. Quadruplex ligands may act as molecular chaperones for tetramolecular quadruplex formation. Nucleic Acids Res.35, 2483–2493 (2007). PubMed PMC

González, V., Guo, K., Hurley, L. & Sun, D. Identification and characterization of nucleolin as a c-myc G-quadruplex-binding protein. J. Biol. Chem.284, 23622–23635 (2009). PubMed PMC

Bates, P. J., Kahlon, J. B., Thomas, S. D., Trent, J. O. & Miller, D. M. Antiproliferative activity of G-rich oligonucleotides correlates with protein binding *. J. Biol. Chem.274, 26369–26377 (1999). PubMed

González, V. & Hurley, L. H. The C-terminus of nucleolin promotes the formation of the c-MYC G-quadruplex and inhibits c-MYC promoter activity. Biochemistry49, 9706–9714 (2010). PubMed PMC

Cangelosi, D. et al. Nucleolin expression has prognostic value in neuroblastoma patients. eBioMedicine85, 104300 (2022). PubMed PMC

Berger, C. M., Gaume, X. & Bouvet, P. The roles of nucleolin subcellular localization in cancer. Biochimie113, 78–85 (2015). PubMed

Tosoni, E. et al. Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription. Nucleic Acids Res.43, 8884–8897 (2015). PubMed PMC

Lista, M. J. et al. Nucleolin directly mediates Epstein-Barr virus immune evasion through binding to G-quadruplexes of EBNA1 mRNA. Nat. Commun.8, 16043 (2017). PubMed PMC

Bian, W. X. et al. Binding of cellular nucleolin with the viral core RNA G-quadruplex structure suppresses HCV replication. Nucleic Acids Res.47, 56–68 (2019). PubMed PMC

Kusov, Y., Tan, J., Alvarez, E., Enjuanes, L. & Hilgenfeld, R. A G-quadruplex-binding macrodomain within the SARS-unique domain is essential for the activity of the SARS-coronavirus replication–transcription complex. Virology484, 313–322 (2015). PubMed PMC

Platella, C., Riccardi, C., Montesarchio, D., Roviello, G. N. & Musumeci, D. G-quadruplex-based aptamers against protein targets in therapy and diagnostics. Biochim. Biophys. Acta BBA - Gen. Subj.1861, 1429–1447 (2017). PubMed PMC

Brázda, V. et al. G4Hunter web application: a web server for G-quadruplex prediction. Bioinformatics35, 3493–3495 (2019). PubMed PMC

Bedrat, A., Lacroix, L. & Mergny, J. L. Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res.44, 1746–1759 (2016). PubMed PMC

Bohálová, N. et al. Analyses of viral genomes for G-quadruplex forming sequences reveal their correlation with the type of infection. Biochimie186, 13–27 (2021). PubMed

Jaubert, C. et al. RNA synthesis is modulated by G-quadruplex formation in Hepatitis C virus negative RNA strand. Sci. Rep.8, 8120 (2018). PubMed PMC

Dobrovolná, M., Mergny, J. L. & Brázda, V. Complete analysis of G-quadruplex forming sequences in the gapless assembly of human chromosome Y. BiochimieS030090842400233510.1016/j.biochi.2024.10.007 (2024). PubMed

Harris, L. M. & Merrick, C. J. G-Quadruplexes in pathogens: a Common Route to Virulence Control? PLoS Pathog. 11, e1004562 (2015). PubMed PMC

Lobo, F. P. et al. Virus-host coevolution: common patterns of Nucleotide Motif usage in Flaviviridae and their hosts. PLoS ONE. 4, e6282 (2009). PubMed PMC

Mihara, T. et al. Linking virus genomes with host taxonomy. Viruses8, 66 (2016). PubMed PMC

Petropoulos, C. & Retroviral Taxonomy Protein Structures, Sequences, and Genetic Maps. In Retroviruses (Cold Spring Harbor Laboratory Press, 1997).

Chen, J. et al. The reservoir of latent HIV. Front. Cell. Infect. Microbiol.12, 945956 (2022). PubMed PMC

Louten, J., Virus & Replication Essent. Hum. Virol. 49–70 doi:10.1016/B978-0-12-800947-5.00004-1. (2016).

Lavezzo, E. et al. G-quadruplex forming sequences in the genome of all known human viruses: a comprehensive guide. PLoS Comput. Biol.14, e1006675 (2018). PubMed PMC

Amrane, S. et al. Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection. Nucleic Acids Res.50, 12328–12343 (2022). PubMed PMC

Perrone, R. et al. Formation of a Unique Cluster of G-Quadruplex structures in the HIV-1 nef Coding Region: implications for antiviral activity. PLoS ONE. 8, e73121 (2013). PubMed PMC

Perrone, R. et al. A dynamic G-Quadruplex region regulates the HIV-1 long terminal repeat promoter. J. Med. Chem.56, 6521–6530 (2013). PubMed PMC

Ruggiero, E. et al. Fused in Liposarcoma Protein, a New Player in the regulation of HIV-1 transcription, binds to known and newly identified LTR G-Quadruplexes. ACS Infect. Dis.8, 958–968 (2022). PubMed PMC

Piekna-Przybylska, D., Sullivan, M. A., Sharma, G. & Bambara, R. A. U3 region in the HIV-1 genome adopts a G-quadruplex structure in its RNA and DNA sequence. Biochemistry53, 2581–2593 (2014). PubMed PMC

Lyonnais, S. G-quartets assembly within a G-rich DNA flap. A possible event at the center of the HIV-1 genome. Nucleic Acids Res.30, 5276–5283 (2002). PubMed PMC

Malet, I. et al. Variability of the HIV-1 3′ polypurine tract (3′PPT) region and implication in integrase inhibitor resistance. J. Antimicrob. Chemother.74, 3440–3444 (2019). PubMed

Perrone, R., Lavezzo, E., Palù, G. & Richter, S. N. Conserved presence of G-quadruplex forming sequences in the long terminal repeat promoter of Lentiviruses. Sci. Rep.7, 2018 (2017). PubMed PMC

Hegedus, L. et al. Werner helicase interacting protein 1 contributes to G-quadruplex processing in human cells. Sci. Rep.14, 15740 (2024). PubMed PMC

Grasso, N. et al. Unveiling the interaction between DNA G-quadruplexes and RG-rich peptides. Int. J. Biol. Macromol.253, 126749 (2023). PubMed

Brázda, V. et al. The amino acid composition of quadruplex binding proteins reveals a Shared Motif and predicts new potential quadruplex interactors. Mol. Basel Switz.23, 2341 (2018). PubMed PMC

Brázda, V., Dobrovolná, M., Bohálová, N. & Mergny, J. L. G-quadruplexes in the evolution of hepatitis B virus. Nucleic Acids Res.51, 7198–7204 (2023). PubMed PMC

Chen, Y., Wei, X., Zhang, G., Holmes, E. C. & Cui, J. Identification and evolution of avian endogenous foamy viruses. Virus Evol.5, vez049 (2019). PubMed PMC

Garant, J. M., Perreault, J. P. & Scott, M. S. Motif independent identification of potential RNA G-quadruplexes by G4RNA screener. Bioinformatics33, 3532–3537 (2017). PubMed PMC

Puig Lombardi, E. & Londoño-Vallejo, A. A guide to computational methods for G-quadruplex prediction. Nucleic Acids Res.48, 1–15 (2020). PubMed PMC

Yang, B. et al. Prediction of DNA i-motifs via machine learning. Nucleic Acids Res.52, 2188–2197 (2024). PubMed PMC

Ruggiero, E. et al. A dynamic i-motif with a duplex stem-loop in the long terminal repeat promoter of the HIV-1 proviral genome modulates viral transcription. Nucleic Acids Res.47, 11057–11068 (2019). PubMed PMC

Gong, J. et al. G-quadruplex structural variations in human genome associated with single-nucleotide variations and their impact on gene activity. Proc. Natl. Acad. Sci. U. S. A. 118, e2013230118 (2021). PubMed PMC

Warner, E. F., Bohálová, N., Brázda, V., Waller, Z. A. E. & Bidula, S. Analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets? Microb. Genomics. 7, 000570 (2021). PubMed PMC

Bartas, M. et al. The Presence and localization of G-Quadruplex forming sequences in the domain of Bacteria. Molecules24, 1711 (2019). PubMed PMC

Hagihara, M., Yoneda, K., Yabuuchi, H., Okuno, Y. & Nakatani, K. A reverse transcriptase stop assay revealed diverse quadruplex formations in UTRs in mRNA. Bioorg. Med. Chem. Lett.20, 2350–2353 (2010). PubMed

Hagihara, M. et al. Antisense-Induced Guanine quadruplexes inhibit reverse transcription by HIV-1 reverse transcriptase. J. Am. Chem. Soc.132, 11171–11178 (2010). PubMed

Tateishi-Karimata, H., Muraoka, T., Kinbara, K. & Sugimoto, N. G-Quadruplexes with Tetra(ethylene glycol)-Modified deoxythymidines are resistant to Nucleases and inhibit HIV-1 reverse transcriptase. ChemBioChem17, 1399–1402 (2016). PubMed

Perrone, R. et al. Synthesis, binding and antiviral properties of Potent Core-Extended Naphthalene diimides Targeting the HIV-1 long terminal repeat promoter G-Quadruplexes. J. Med. Chem.58, 9639–9652 (2015). PubMed PMC

Pávová, M. et al. Helquat dyes targeting G-quadruplexes as a new class of anti-HIV-1 inhibitors. Sci. Rep.13, 6096 (2023). PubMed PMC

The UniProt Consortium. UniProt: the Universal protein knowledgebase in 2023. Nucleic Acids Res.51, D523–D531 (2023). PubMed PMC

Garant, J. M., Perreault, J. P. & Scott, M. S. G4RNA screener web server: user focused interface for RNA G-quadruplex prediction. Biochimie151, 115–118 (2018). PubMed

Sahakyan, A. B. et al. Machine learning model for sequence-driven DNA G-quadruplex formation. Sci. Rep.7, 14535 (2017). PubMed PMC

Robinson, J. T., Thorvaldsdottir, H., Turner, D. & Mesirov, J. P. igv.js: an embeddable JavaScript implementation of the Integrative Genomics viewer (IGV). Bioinformatics39, btac830 (2023). PubMed PMC