Antiretroviral APOBEC3 cytidine deaminases alter HIV-1 provirus integration site profiles

Hannah O. Ajoge, Tyler M. Renner, Kasandra Bélanger, Matthew Greig, Samar Dankar, Hinissan P. Kohio, Macon D. Coleman, Emmanuel Ndashimye, Eric J. Arts, Marc-André Langlois () and Stephen D. Barr ()
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Hannah O. Ajoge: Western University, Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology
Tyler M. Renner: University of Ottawa
Kasandra Bélanger: University of Ottawa
Matthew Greig: University of Ottawa
Samar Dankar: University of Ottawa
Hinissan P. Kohio: Western University, Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology
Macon D. Coleman: Western University, Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology
Emmanuel Ndashimye: Western University, Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology
Eric J. Arts: Western University, Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology
Marc-André Langlois: University of Ottawa
Stephen D. Barr: Western University, Schulich School of Medicine and Dentistry, Department of Microbiology and Immunology

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: Abstract APOBEC3 (A3) proteins are host-encoded deoxycytidine deaminases that provide an innate immune barrier to retroviral infection, notably against HIV-1. Low levels of deamination are believed to contribute to the genetic evolution of HIV-1, while intense catalytic activity of these proteins can induce catastrophic hypermutation in proviral DNA leading to near-total HIV-1 restriction. So far, little is known about how A3 cytosine deaminases might impact HIV-1 proviral DNA integration sites in human chromosomal DNA. Using a deep sequencing approach, we analyze the influence of catalytic active and inactive APOBEC3F and APOBEC3G on HIV-1 integration site selections. Here we show that DNA editing is detected at the extremities of the long terminal repeat regions of the virus. Both catalytic active and non-catalytic A3 mutants decrease insertions into gene coding sequences and increase integration sites into SINE elements, oncogenes and transcription-silencing non-B DNA features. Our data implicates A3 as a host factor influencing HIV-1 integration site selection and also promotes what appears to be a more latent expression profile.

Date: 2023
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DOI: 10.1038/s41467-022-35379-y

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