Cited by 164HIV Research and TreatmentVirus-based gene therapy researchHIV/AIDS drug development and treatment

Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites

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Holman, Alexander G., Coffin, John M.·2005·Proceedings of the National Academy of Sciences

Abstract

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.

Integrity signals

Registry

Crossref · 10.1073/pnas.0501646102

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12 of 12 references verified0 citation errors · 0 not checkable

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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).”

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Authors
Holman, A. G., & Coffin, J. M.
Affiliations
Tufts University (US)
Corresponding author
Coffin, John M.
Venue
Proceedings of the National Academy of Sciences
Published
2005-03-31
Volume
102
Issue
17
Pages
6103-6107
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
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
Open access
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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