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Cited by 78Virus-based gene therapy researchHIV Research and TreatmentHIV/AIDS drug development and treatment

Retroviral integration site selection

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Desfarges, Sébastien, Ciuffi, Angela·2010·Viruses
DOI 10.3390/v2010111PMC PMC3185549
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Abstract

The stable insertion of a copy of their genome into the host cell genome is an essential step of the life cycle of retroviruses. The site of viral DNA integration, mediated by the viral-encoded integrase enzyme, has important consequences for both the virus and the host cell. The analysis of retroviral integration site distribution was facilitated by the availability of the human genome sequence, revealing the non-random feature of integration site selection and identifying different favored and disfavored genomic locations for individual retroviruses. This review will summarize the current knowledge about retroviral differences in their integration site preferences as well as the mechanisms involved in this process.

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  • Various retroviruses have adapted to favor different integration sites depending on the chromatin state.

    “Thus, various retroviruses have adapted to favor different integration sites depending upon the chromatin state (Desfarges and Ciuffi 2010).”

    From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Desfarges and Ciuffi 2010

    The ‘Integration targeting in vivo’ section reports distinct integration-site preferences among retroviruses, and ‘Epigenetic modifications and integration targeting’ associates some sites with marks of active or repressed chromatin (no page numbers provided). But ‘The chromatin accessibility model’ says chromatin accessibility cannot explain the differences among retroviruses; the paper does not establish that they adapted to favor different sites depending on chromatin state. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Sequences internal to the terminal CA and TG dinucleotides are not well conserved, even though they are needed for ideal IN activity during integration.

    “However, the sequences internal to these dinucleotides are not well conserved, even though they are needed for ideal IN activity during integration (Bushman and Craigie 1991, Brown 1997, Desfarges and Ciuffi 2010, Ali et al. 2016).”

    From Beyond reverse transcription: molecular mechanisms and emerging paradigms in retroviral replication (2026) · cites this paper as Desfarges and Ciuffi 2010

    The “Integration targeting in vitro” section says that integrase recognizes a donor DNA mimicking a viral terminal sequence, but it does not address whether sequences internal to terminal CA and TG dinucleotides are poorly conserved or needed for optimal integrase activity. Searches for those dinucleotides and for conservation of viral DNA ends found no passage establishing the claim. (LLM, conf=0.72)

    Experimental — accuracy not yet measured

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Authors
Desfarges, S., & Ciuffi, A.
Affiliations
Centre Hospitalier Universitaire Vaudois (CH)
Corresponding author
Ciuffi, Angela
ORCID
Ciuffi, Angela
Venue
Viruses
Publisher
MDPI AG
Published
2010-01-12
Volume
2
Issue
1
Pages
111-130
ISSN
1999-4915 (ISSN-L)
DOI
10.3390/v2010111
PMC
PMC3185549
OpenAlex
W1967301672
Cited by
78
References
11
Citations by year
2026: 1 · 2025: 7 · 2024: 6 · 2023: 2 · 2022: 3 · 2021: 7 · 2020: 4 · 2019: 4 · 2018: 4 · 2017: 4 · 2016: 5 · 2015: 7 · 2014: 3 · 2013: 9 · 2012: 4
FWCI
3.60
Type
journal article
Language
en
Open access
Licence
Locations
  • Viruses (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • SERVAL (Université de Lausanne) (publishedVersion, other-oa)
  • IRIS (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • National Science Foundation
  • Novartis Foundation
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (120553, 3100A0)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
  • Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
  • Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
Keywords
retroviral integration, integration site selection, integrase, human genome sequence, retrovirus-host interactions

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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