Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites
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To investigate retroviral integration targeting on a nucleotide scale, we examined the base frequencies directly surrounding cloned in vivo HIV-1, murine leukemia virus, and avian sarcoma/leukosis virus integrations. Base preferences of up to 2-fold the expected frequencies were found for three viruses, representing P values down to <10 -100 and defining what appear to be preferred integration sequences. Offset symmetry reflecting the topology of the integration reaction was found for HIV-1 and avian sarcoma/leukosis virus but not murine leukemia virus, suggesting fundamental differences in the way different retroviral integration complexes interact with host-cell DNA.
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A weak palindromic (pal) motif is often present in target DNA sequences recognized by IN.
“Briefly, there seems to be a consensus, especially noticed in the retroviral integration site alignments, that a weak pal motif is often present in the target DNA sequences that are recognized by IN (Stevens and Griffith 1996, Holman and Coffin 2005, Wu et al. 2005, Miklík et al. 2023).”
From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Holman and Coffin 2005
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Matrix attachment regions as targets for retroviral integration
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Engineered Sleeping Beauty transposase redirects transposon integration away from genes
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Sites of retroviral DNA integration: From basic research to clinical applications
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- Authors
- Holman, A. G., & Coffin, J. M.
- Affiliations
- Tufts University (US)
- Corresponding author
- Coffin, John M.
- ORCID
- Coffin, John M.
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2005-03-31
- Volume
- 102
- Issue
- 17
- Pages
- 6103-6107
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC1087937
- OpenAlex
- W2026422480
- Cited by
- 164
- References
- 12
- Citations by year
- 2026: 1 · 2025: 4 · 2023: 4 · 2022: 5 · 2021: 5 · 2020: 3 · 2019: 6 · 2018: 3 · 2017: 6 · 2016: 17 · 2015: 11 · 2014: 7 · 2013: 7 · 2012: 12
- FWCI
- 4.88
- Type
- journal article
- Language
- en
- Update notices
- correction (2005-04-26)
- Open access
- green
- dx.doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed (publishedVersion)
- Funders
- American Cancer Society
- F. M. Kirby Foundation
- University of Pennsylvania
- James N. Kirby Foundation
- National Institutes of Health (NIH T32)
- National Human Genome Research Institute
- National Cancer Institute (T32 CA65441, T32CA065441, R01-CA-92192, R01CA092192)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
- Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
- Keywords
- retroviral integration, integration site selection, HIV-1, murine leukemia virus, host cell DNA, sequence symmetry
- MeSH terms
- Alpharetrovirus, Base Composition, Base Sequence, Cloning, Molecular, HeLa Cells, Humans, HIV-1, Virus Integration
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