Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions

Carlotta Penzo; Ilayda Özel; Moreno Martinovic; Maja Kuzman; Dunja Glavas; Mia Stanic; Thomas Reichenbach; Thorsten G Müller; Mona Rheinberger; Negar Godarzi; Delphine Lapaillerie; Bruno Srezovic; Maria Chiara dell'Oca; Laura C Lange; Lopamudra Sadhu; Ines J de Castro; Iart Luca Shytaj; Mattia Forcato; Vibor Laketa; Silvio Bicciato; Kristian Vlahovicek; Oliver T Fackler; Bojana Lucic; Vlad Pena; Hans-Georg Kräusslich; Vincent Parissi; Marina Lusic

doi:10.1038/s41564-025-02089-2

Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions

Carlotta Penzo
, Ilayda Özel
, Moreno Martinovic
, Maja Kuzman
, Dunja Glavas
, Mia Stanic
, Thomas Reichenbach
, Thorsten G Müller
, Mona Rheinberger
, Negar Godarzi
, Delphine Lapaillerie
, Bruno Srezovic
, Maria Chiara dell'Oca
, Laura C Lange
, Lopamudra Sadhu
, Ines J de Castro
, Iart Luca Shytaj
, Mattia Forcato
, Vibor Laketa
, Silvio Bicciato

Kristian Vlahovicek, Oliver T Fackler, Bojana Lucic, Vlad Pena, Hans-Georg Kräusslich, Vincent Parissi, Marina Lusic^*

^*Corresponding author for this work

Research output: Contribution to journal › Article (Academic Journal) › peer-review

3 Citations (Scopus)

40 Downloads (Pure)

Abstract

HIV-1 integration into host chromosomes, essential for viral replication, is catalysed by viral integrase (IN). IN recurrently targets intronic regions of transcriptionally active genes, but a detailed understanding of this process is still unclear. Here, using ex vivo activated human primary CD4⁺T cells, we find that genomic RNA:DNA hybrids (R-loops) preferentially map to intronic regions of active genes that are typical HIV-1 integration sites. IN binds R-loops and their resolution enhances viral integration in vitro. We identify Aquarius (AQR), the splicing RNA helicase of the pentameric intron binding complex (IBC), which associates with IN and show that its RNA:DNA helicase activity promotes integration into hybrid substrates in vitro. Knockout of AQR in primary CD4⁺ T cells impaired overall integration efficiency, while sequencing of remaining integrations mapped them to intergenic and R-loop distal regions. These findings may have important implications for HIV-1 latency and reactivation and may thus identify novel therapeutic targets.

Original language	English
Pages (from-to)	2306–2322
Number of pages	17
Journal	Nature Microbiology
Volume	10
Issue number	9
Early online date	20 Aug 2025
DOIs	https://doi.org/10.1038/s41564-025-02089-2
Publication status	Published - 1 Sept 2025

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Publisher Copyright:
© The Author(s), under exclusive licence to Springer Nature Limited 2025.

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Penzo, C., Özel, I., Martinovic, M., Kuzman, M., Glavas, D., Stanic, M., Reichenbach, T., Müller, T. G., Rheinberger, M., Godarzi, N., Lapaillerie, D., Srezovic, B., dell'Oca, M. C., Lange, L. C., Sadhu, L., de Castro, I. J., Shytaj, I. L., Forcato, M., Laketa, V., ... Lusic, M. (2025). Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions. Nature Microbiology, 10(9), 2306–2322. https://doi.org/10.1038/s41564-025-02089-2

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title = "Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions",

abstract = "HIV-1 integration into host chromosomes, essential for viral replication, is catalysed by viral integrase (IN). IN recurrently targets intronic regions of transcriptionally active genes, but a detailed understanding of this process is still unclear. Here, using ex vivo activated human primary CD4+T cells, we find that genomic RNA:DNA hybrids (R-loops) preferentially map to intronic regions of active genes that are typical HIV-1 integration sites. IN binds R-loops and their resolution enhances viral integration in vitro. We identify Aquarius (AQR), the splicing RNA helicase of the pentameric intron binding complex (IBC), which associates with IN and show that its RNA:DNA helicase activity promotes integration into hybrid substrates in vitro. Knockout of AQR in primary CD4+ T cells impaired overall integration efficiency, while sequencing of remaining integrations mapped them to intergenic and R-loop distal regions. These findings may have important implications for HIV-1 latency and reactivation and may thus identify novel therapeutic targets.",

author = "Carlotta Penzo and Ilayda {\"O}zel and Moreno Martinovic and Maja Kuzman and Dunja Glavas and Mia Stanic and Thomas Reichenbach and M{\"u}ller, \{Thorsten G\} and Mona Rheinberger and Negar Godarzi and Delphine Lapaillerie and Bruno Srezovic and dell'Oca, \{Maria Chiara\} and Lange, \{Laura C\} and Lopamudra Sadhu and \{de Castro\}, \{Ines J\} and Shytaj, \{Iart Luca\} and Mattia Forcato and Vibor Laketa and Silvio Bicciato and Kristian Vlahovicek and Fackler, \{Oliver T\} and Bojana Lucic and Vlad Pena and Hans-Georg Kr{\"a}usslich and Vincent Parissi and Marina Lusic",

note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive licence to Springer Nature Limited 2025.",

year = "2025",

month = sep,

day = "1",

doi = "10.1038/s41564-025-02089-2",

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Penzo, C, Özel, I, Martinovic, M, Kuzman, M, Glavas, D, Stanic, M, Reichenbach, T, Müller, TG, Rheinberger, M, Godarzi, N, Lapaillerie, D, Srezovic, B, dell'Oca, MC, Lange, LC, Sadhu, L, de Castro, IJ, Shytaj, IL, Forcato, M, Laketa, V, Bicciato, S, Vlahovicek, K, Fackler, OT, Lucic, B, Pena, V, Kräusslich, H-G, Parissi, V & Lusic, M 2025, 'Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions', Nature Microbiology, vol. 10, no. 9, pp. 2306–2322. https://doi.org/10.1038/s41564-025-02089-2

TY - JOUR

T1 - Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions

AU - Penzo, Carlotta

AU - Özel, Ilayda

AU - Martinovic, Moreno

AU - Kuzman, Maja

AU - Glavas, Dunja

AU - Stanic, Mia

AU - Reichenbach, Thomas

AU - Müller, Thorsten G

AU - Rheinberger, Mona

AU - Godarzi, Negar

AU - Lapaillerie, Delphine

AU - Srezovic, Bruno

AU - dell'Oca, Maria Chiara

AU - Lange, Laura C

AU - Sadhu, Lopamudra

AU - de Castro, Ines J

AU - Shytaj, Iart Luca

AU - Forcato, Mattia

AU - Laketa, Vibor

AU - Bicciato, Silvio

AU - Vlahovicek, Kristian

AU - Fackler, Oliver T

AU - Lucic, Bojana

AU - Pena, Vlad

AU - Kräusslich, Hans-Georg

AU - Parissi, Vincent

AU - Lusic, Marina

PY - 2025/9/1

Y1 - 2025/9/1

N2 - HIV-1 integration into host chromosomes, essential for viral replication, is catalysed by viral integrase (IN). IN recurrently targets intronic regions of transcriptionally active genes, but a detailed understanding of this process is still unclear. Here, using ex vivo activated human primary CD4+T cells, we find that genomic RNA:DNA hybrids (R-loops) preferentially map to intronic regions of active genes that are typical HIV-1 integration sites. IN binds R-loops and their resolution enhances viral integration in vitro. We identify Aquarius (AQR), the splicing RNA helicase of the pentameric intron binding complex (IBC), which associates with IN and show that its RNA:DNA helicase activity promotes integration into hybrid substrates in vitro. Knockout of AQR in primary CD4+ T cells impaired overall integration efficiency, while sequencing of remaining integrations mapped them to intergenic and R-loop distal regions. These findings may have important implications for HIV-1 latency and reactivation and may thus identify novel therapeutic targets.

AB - HIV-1 integration into host chromosomes, essential for viral replication, is catalysed by viral integrase (IN). IN recurrently targets intronic regions of transcriptionally active genes, but a detailed understanding of this process is still unclear. Here, using ex vivo activated human primary CD4+T cells, we find that genomic RNA:DNA hybrids (R-loops) preferentially map to intronic regions of active genes that are typical HIV-1 integration sites. IN binds R-loops and their resolution enhances viral integration in vitro. We identify Aquarius (AQR), the splicing RNA helicase of the pentameric intron binding complex (IBC), which associates with IN and show that its RNA:DNA helicase activity promotes integration into hybrid substrates in vitro. Knockout of AQR in primary CD4+ T cells impaired overall integration efficiency, while sequencing of remaining integrations mapped them to intergenic and R-loop distal regions. These findings may have important implications for HIV-1 latency and reactivation and may thus identify novel therapeutic targets.

U2 - 10.1038/s41564-025-02089-2

DO - 10.1038/s41564-025-02089-2

M3 - Article (Academic Journal)

C2 - 40836041

SN - 2058-5276

VL - 10

SP - 2306

EP - 2322

JO - Nature Microbiology

JF - Nature Microbiology

IS - 9

ER -

Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions

Abstract

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