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| Status |
Public on Nov 05, 2024 |
| Title |
Human immunodeficiency virus-1 targets genomic R-loops of the host for integration [IS-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Although HIV-1 integration sites are considered to favor active transcription units in the human genome, high-resolution analysis of individual HIV-1 integration sites have shown that the virus can integrate in a variety of host genomic locations, including non-genic regions, challenging the traditional understanding of HIV-1 integration site selection. Here, we showed that HIV-1 targets R-loops, a genomic structure made up of DNA–RNA hybrids, for integration. HIV-1 initiates the formation of R-loops in both genic and non-genic regions of the host genome and preferentially integrates into regions of HIV-1-induced R-loops. Using a cell model that can independently control transcriptional activity and R-loop formation, we demonstrated that the presence of R-loops, regardless of transcriptional activity, directs HIV-1 integration targeting sites. We also found that HIV-1 integrase proteins bind to the host genomic R-loops. These findings provide fundamental insights into the mechanisms of retroviral integration and the new strategies of antiretroviral therapy against HIV-1 latent infection.
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| Overall design |
HeLa, CD4+ and Jurkat cells were infected with VSV-G-pseudotyped HIV-1-EGFP and harvested at 5 d post infection (dpi) for HIV-1 integration site sequencing
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| Contributor(s) |
Park K, Lee D, Kim S, Ahn K |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Nov 04, 2024 |
| Last update date |
Nov 06, 2024 |
| Contact name |
Dohoon Lee |
| E-mail(s) |
[email protected]
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| Organization name |
Seoul National University
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| Department |
Bioinformatics Institute
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| Street address |
1, Gwanak-ro, Gwanak-gu
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| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
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| Platforms (1) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA1181859 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE281026_RAW.tar |
3.6 Mb |
(http)(custom) |
TAR (of BED) |
| GSE281026_vDNA_integration_seq_result.csv.gz |
670 b |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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