Asymmetric distribution of G-quadruplex forming sequences in
genomes of retroviruses

J 2025

Asymmetric distribution of G-quadruplex forming sequences in genomes of retroviruses

KLEDUS, Filip; Michaela DOBROVOLNA; Jean-Louis MERGNY and Václav BRÁZDA

Basic information

Original name

Asymmetric distribution of G-quadruplex forming sequences in genomes of retroviruses

Authors

KLEDUS, Filip (203 Czech Republic, belonging to the institution); Michaela DOBROVOLNA (203 Czech Republic); Jean-Louis MERGNY (250 France) and Václav BRÁZDA (203 Czech Republic, guarantor)

Edition

Nature Scientific Reports, BERLIN, NATURE PORTFOLIO, 2025, 2045-2322

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Germany

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Impact factor

Impact factor: 3.800 in 2023

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1038/s41598-024-82613-2

UT WoS

001390050200002

EID Scopus

2-s2.0-85213943520

Keywords in English

G-quadruplex; Retroviral genome; Bioinformatics; Persistent infection; G4Hunter

Abstract

V originále

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.

Cite

KLEDUS, Filip; Michaela DOBROVOLNA; Jean-Louis MERGNY and Václav BRÁZDA. Asymmetric distribution of G-quadruplex forming sequences in genomes of retroviruses. Nature Scientific Reports. BERLIN: NATURE PORTFOLIO, 2025, vol. 15, No 1, p. 1-12. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-024-82613-2.

@article{2478593,
   author = {Kledus, Filip and Dobrovolna, Michaela and Mergny, JeanandLouis and Brázda, Václav},
   article_location = {BERLIN},
   article_number = {1},
   doi = {http://dx.doi.org/10.1038/s41598-024-82613-2},
   keywords = {G-quadruplex; Retroviral genome; Bioinformatics; Persistent infection; G4Hunter},
   language = {eng},
   issn = {2045-2322},
   journal = {Nature Scientific Reports},
   title = {Asymmetric distribution of G-quadruplex forming sequences in genomes of retroviruses},
   url = {https://www.nature.com/articles/s41598-024-82613-2},
   volume = {15},
   year = {2025}
}

TY  - JOUR
ID  - 2478593
AU  - Kledus, Filip - Dobrovolna, Michaela - Mergny, Jean-Louis - Brázda, Václav
PY  - 2025
TI  - Asymmetric distribution of G-quadruplex forming sequences in genomes of retroviruses
JF  - Nature Scientific Reports
VL  - 15
IS  - 1
SP  - 1-12
EP  - 1-12
PB  - NATURE PORTFOLIO
SN  - 20452322
KW  - G-quadruplex
KW  - Retroviral genome
KW  - Bioinformatics
KW  - Persistent infection
KW  - G4Hunter
UR  - https://www.nature.com/articles/s41598-024-82613-2
N2  - 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.
ER  -

KLEDUS, Filip; Michaela DOBROVOLNA; Jean-Louis MERGNY and Václav BRÁZDA. Asymmetric distribution of G-quadruplex forming sequences in genomes of retroviruses. \textit{Nature Scientific Reports}. BERLIN: NATURE PORTFOLIO, 2025, vol.~15, No~1, p.~1-12. ISSN~2045-2322. Available from: https://dx.doi.org/10.1038/s41598-024-82613-2.

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