# DNA damage induced by HIV-1 Vpr triggers epigenetic remodeling and transcriptional programs to enhance virus transcription and latency reactivation

**Authors:** Nicholas Saladino, Emily Leavitt, Hoi Tong Wong, Jae-Hoon Ji, Diako Ebrahimi, Daniel J. Salamango, Melissa Vazquez Hernandez, Melissa Vazquez Hernandez, Melissa Vazquez Hernandez, Melissa Vazquez Hernandez

PMC · DOI: 10.1371/journal.pbio.3003621 · PLOS Biology · 2026-02-02

## TL;DR

This study shows that HIV-1 uses a protein called Vpr to cause DNA damage, which helps the virus become more active and escape dormancy, offering new treatment possibilities.

## Contribution

The study reveals that Vpr-induced DNA damage promotes epigenetic changes and transcriptional programs that enhance HIV-1 transcription and latency reactivation.

## Key findings

- Vpr induces DNA damage responses that trigger epigenetic remodeling and enhance HIV-1 promoter activity.
- Vpr exists in two pools: one in the nucleus associated with chromatin and one in the cytoplasm linked to an E3-ubiquitin ligase.
- Vpr-induced DDR and epigenetic activities are present in global HIV-1 subtypes and patient isolates.

## Abstract

Hijacking of host DNA damage repair (DDR) pathways to facilitate virus replication is broadly conserved amongst diverse viral families. It has been well established that the HIV-1 accessory protein Vpr induces constitutive DDR signaling and G2/M cell cycle arrest, but the virologic function of this activity remains unclear. Here, we use a combination of functional, pharmacologic, biochemical, and genetic approaches to establish that virion-associated and de novo Vpr proteins induce DDR responses that trigger global epigenetic remodeling and activation of transcription programs to enhance HIV-1 promoter activity during acute infection and reactivation from latency. Functional, genetic, and bimolecular fluorescence complementation experiments reveal that Vpr segregates into two functionally discrete pools—a multimeric pool in the nucleus associated with chromatin and a monomeric pool in the cytoplasm associated with a host E3-ubiquitin ligase. Vpr-induced DDR and epigenetic remodeling activities are present in common HIV-1 subtypes circulating globally and in patient-derived isolates.

HIV-1 induces a persistent DNA damage response through Vpr, but whether this affects the viral cycle has remained unclear. This study shows that Vpr-driven DNA damage promotes epigenetic remodeling and transcriptional programs that enhance HIV-1 transcription and latency reactivation, identifying a possible target for new treatment strategies.

## Linked entities

- **Genes:** vpr (Vpr) [NCBI Gene 155807]
- **Proteins:** vpr (Vpr)

## Full-text entities

- **Genes:** RAD23A (RAD23 nucleotide excision repair protein A) [NCBI Gene 5886] {aka HHR23A, HR23A}, HLA-T (major histocompatibility complex, class I, T (pseudogene)) [NCBI Gene 352964] {aka HLA-16}, PRKDC (protein kinase, DNA-activated, catalytic subunit) [NCBI Gene 5591] {aka DNA-PKC, DNA-PKcs, DNAPK, DNAPKc, DNPK1, HYRC}, vpr (Vpr) [NCBI Gene 155807], DDB1 (damage specific DNA binding protein 1) [NCBI Gene 1642] {aka DDBA, UV-DDB1, WHIKERS, XAP1, XPCE, XPE}, RNASEH1 (ribonuclease H1) [NCBI Gene 246243] {aka H1RNA, PEOB2, RNH1}, CBLL2 (Cbl proto-oncogene like 2) [NCBI Gene 158506] {aka CT138, HAKAIL, ZNF645}, TAT (tyrosine aminotransferase) [NCBI Gene 6898], KAT2A (lysine acetyltransferase 2A) [NCBI Gene 2648] {aka GCN5, GCN5L2, PCAF-b, hGCN5}, NFKB1 (nuclear factor kappa B subunit 1) [NCBI Gene 4790] {aka CVID12, EBP-1, KBF1, NF-kB, NF-kB1, NF-kappa-B1}, CHEK1 (checkpoint kinase 1) [NCBI Gene 1111] {aka CHK1, OZEMA21}, SP1 (Sp1 transcription factor) [NCBI Gene 6667], H2BC21 (H2B clustered histone 21) [NCBI Gene 8349] {aka GL105, H2B, H2B-GL105, H2B.1, H2BE, H2BFQ}, ATM (ATM serine/threonine kinase) [NCBI Gene 472] {aka AT1, ATA, ATC, ATD, ATDC, ATE}, HDAC9 (histone deacetylase 9) [NCBI Gene 9734] {aka HD7, HD7b, HD9, HDAC, HDAC7B, HDAC9B}, IKBKG (inhibitor of nuclear factor kappa B kinase regulatory subunit gamma) [NCBI Gene 8517] {aka AMCBX1, EDAID1, FIP-3, FIP3, Fip3p, IKK-gamma}, H2AX (H2A.X variant histone) [NCBI Gene 3014] {aka H2A.X, H2A/X, H2AFX}, RNF112 (ring finger protein 112) [NCBI Gene 7732] {aka BFP, ZNF179}, CSF2 (colony stimulating factor 2) [NCBI Gene 1437] {aka CSF, GMCSF}, CHEK2 (checkpoint kinase 2) [NCBI Gene 11200] {aka CDS1, CHK2, HuCds1, LFS2, PP1425, RAD53}, RELA (RELA proto-oncogene, NF-kB subunit) [NCBI Gene 5970] {aka AIF3BL3, CMCU, NFKB3, p65}, Nef [NCBI Gene 156110], vif (Vif) [NCBI Gene 155459], NUP98 (nucleoporin 98 and 96 precursor) [NCBI Gene 4928] {aka ADIR2, NUP196, NUP96, Nup98-96}, DCAF1 (DDB1 and CUL4 associated factor 1) [NCBI Gene 9730] {aka RIP, VPRBP}, POLR2A (RNA polymerase II subunit A) [NCBI Gene 5430] {aka NEDHIB, POLR2, POLRA, RPB1, RPBh1, RPO2}, MUL1 (mitochondrial E3 ubiquitin protein ligase 1) [NCBI Gene 79594] {aka C1orf166, GIDE, MAPL, MULAN, RNF218}, ATR (ATR checkpoint kinase) [NCBI Gene 545] {aka FCTCS, FRP1, MEC1, SCKL, SCKL1}, Vpu [NCBI Gene 155945], JUN (Jun proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 3725] {aka AP-1, AP1, c-Jun, cJUN, p39}, YWHAQ (tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta) [NCBI Gene 10971] {aka 14-3-3, 1C5, HS1}
- **Diseases:** acute (MESH:D000208), HIV-1 infection (MESH:D015490), virus (MESH:D014777), MDMs (MESH:D055501), Infection (MESH:D007239)
- **Chemicals:** oil (MESH:D009821), NU6027 (MESH:C475622), NaCl (MESH:D012965), H2O (MESH:D014867), DTT (MESH:D004229), Digitonin (MESH:D004072), glycerol (MESH:D005990), NU7026 (MESH:C479235), polyvinylidene fluoride (MESH:C024865), chloroform (MESH:D002725), PFA (MESH:C003043), Raltegravir (MESH:D000068898), Triton X-100 (MESH:D017830), penicillin (MESH:D010406), streptomycin (MESH:D013307), PI (MESH:D011419), ethanol (MESH:D000431), EDTA (MESH:D004492), caffeine (MESH:D002110), puromycin (MESH:D011691), hygromycin (MESH:C026273), AZT (MESH:D015215), isopropanol (MESH:D019840), DMEM medium (-), Triptolide (MESH:C001899), NU7441 (MESH:C499693), ATRi (MESH:C069225), Etravirine (MESH:C451734), methanol (MESH:D000432), DAPI (MESH:C007293), deoxycholate (MESH:D003840), bromophenol blue (MESH:D001978), PEI (MESH:D011094), PMA (MESH:D013755), Alexa Fluor 488 (MESH:C000711379), etoposide (MESH:D005047), TRizol (MESH:C411644), SDS (MESH:D012967)
- **Species:** Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090], Human immunodeficiency virus 1 (no rank) [taxon 11676]
- **Mutations:** S79E, Y15, S79, M glycine for 2, I31A, R33A, S79A, T2A, Q65R, Y15R, H71R, Y15H
- **Cell lines:** HIVNL4-3 — Anopheles gambiae (African malaria mosquito), Spontaneously immortalized cell line (CVCL_Z622), HeLa — Homo sapiens (Human), Human papillomavirus-related endocervical adenocarcinoma, Cancer cell line (CVCL_0030), CEM — Homo sapiens (Human), Childhood T acute lymphoblastic leukemia, Cancer cell line (CVCL_0207), J-Lat 10.6 — Homo sapiens (Human), Childhood T acute lymphoblastic leukemia, Cancer cell line (CVCL_8281), J-Lat — Homo sapiens (Human), Childhood T acute lymphoblastic leukemia, Cancer cell line (CVCL_8280), U2OS — Homo sapiens (Human), Osteosarcoma, Cancer cell line (CVCL_0042), U1 — Homo sapiens (Human), Adult acute monocytic leukemia, Cancer cell line (CVCL_M769), H-Lats — Mus musculus (Mouse), Embryonic stem cell (CVCL_RZ32), THP1 — Homo sapiens (Human), Childhood acute monocytic leukemia, Cancer cell line (CVCL_0006), Thp1 — Homo sapiens (Human), Erythromelalgia, Induced pluripotent stem cell (CVCL_9S41), S2 — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z232), HEK293T — Homo sapiens (Human), Transformed cell line (CVCL_0063)

## Full text

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## Figures

8 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12875578/full.md

## References

102 references — full list in the complete paper: https://tomesphere.com/paper/PMC12875578/full.md

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Source: https://tomesphere.com/paper/PMC12875578