Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains
HIV-1 encounters the hierarchically organized host chromatin to stably integrate and persist in anatomically distinct latent reservoirs. The contribution of genome organization in HIV-1 infection has been largely understudied across different HIV-1 targets. Here, we determine HIV-1 integration sites...
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| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
13 February 2023
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| In: |
Cell reports
Year: 2023, Volume: 42, Issue: 2, Pages: 1-27 |
| ISSN: | 2211-1247 |
| DOI: | 10.1016/j.celrep.2023.112110 |
| Online Access: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1016/j.celrep.2023.112110 Verlag, lizenzpflichtig, Volltext: https://www.sciencedirect.com/science/article/pii/S2211124723001213 |
| Author Notes: | Mona Rheinberger, Ana Luisa Costa, Martin Kampmann, Dunja Glavas, Iart Luca Shytaj, Sheetal Sreeram, Carlotta Penzo, Nadine Tibroni, Yoelvis Garcia-Mesa, Konstantin Leskov, Oliver T. Fackler, Kristian Vlahovicek, Jonathan Karn, Bojana Lucic, Carl Herrmann, Marina Lusic |
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| 520 | |a HIV-1 encounters the hierarchically organized host chromatin to stably integrate and persist in anatomically distinct latent reservoirs. The contribution of genome organization in HIV-1 infection has been largely understudied across different HIV-1 targets. Here, we determine HIV-1 integration sites (ISs), associate them with chromatin and expression signatures at different genomic scales in a microglia cell model, and profile them together with the primary T cell reservoir. HIV-1 insertions into introns of actively transcribed genes with IS hotspots in genic and super-enhancers, characteristic of blood cells, are maintained in the microglia cell model. Genome organization analysis reveals dynamic CCCTC-binding factor (CTCF) clusters in cells with active and repressed HIV-1 transcription, whereas CTCF removal impairs viral integration. We identify CTCF-enriched topologically associated domain (TAD) boundaries with signatures of transcriptionally active chromatin as HIV-1 integration determinants in microglia and CD4+ T cells, highlighting the importance of host genome organization in HIV-1 infection. | ||
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