The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites
Open accessAbstract
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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“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
Citations
Cites
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
The UCSC Genome Browser Database
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg129 · Cited by 1,890
HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots
Schröder, A. R. W., Shinn, P., Chen, H., Berry, C., Ecker, J. R., & Bushman, F. (2002) · Cell · doi:10.1016/s0092-8674(02)00864-4 · Cited by 1,832
Transcription Start Regions in the Human Genome Are Favored Targets for MLV Integration
Wu, X., Li, Y., Crise, B., & Burgess, S. M. (2003) · Science · doi:10.1126/science.1083413 · Cited by 1,305
Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences
Mitchell, R., Beitzel, B. F., Schröder, A. R. W., Shinn, P., Chen, H., Berry, C. C., Ecker, J. R., & Bushman, F. D. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020234 · Cited by 1,002
Genome-Wide Analyses of Avian Sarcoma Virus Integration Sites
Narezkina, A., Taganov, K. D., Litwin, S., Stoyanova, R. S., Hayashi, J., Seeger, C., Skalka, A. M., & Katz, R. A. (2004) · Journal of Virology · doi:10.1128/jvi.78.21.11656-11663.2004 · Cited by 157
Carteau, S., Hoffmann, C. J., & Bushman, F. D. (1998) · Journal of Virology · doi:10.1128/jvi.72.5.4005-4014.1998 · Cited by 144
Concerted integration of retrovirus-like DNA by human immunodeficiency virus type 1 integrase
Goodarzi, G., Im, G., Brackmann, K. H., & Grandgenett, D. P. (1995) · Journal of Virology · doi:10.1128/jvi.69.10.6090-6097.1995 · Cited by 84
Central Core Domain of Retroviral Integrase Is Responsible for Target Site Selection
hio Shibagaki, Y., & Chow, S. A. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.13.8361 · Cited by 73
Cited by
Sorted by citations
Wang, G. P., Ciuffi, A., Leipzig, J., Berry, C. C., & Bushman, F. D. (2007) · Genome Research · doi:10.1101/gr.6286907 · Cited by 457
“A weakly conserved inverted repeat sequence from base position 3 to 7 was observed, matching that reported previously (Stevens and Griffith 1996; Carteau et al. 1998; Holman and Coffin 2005; Wu et al. 2005; Berry et al. 2006).”
Shun, M.-C., Raghavendra, N. K., Vandegraaff, N., Daigle, J. E., Hughes, S., Kellam, P., Cherepanov, P., & Engelman, A. (2007) · Genes & Development · doi:10.1101/gad.1565107 · Cited by 467
“Taken together, we conclude that IN is structurally and functionally intact in the absence of cellular LEDGF/p75 and, by extension, that the propensity for different retroviruses to integrate at weakly preferred target DNA sequences (Holman and Coffin 2005) is mechanistically separable from the targeting machineries t…”
BackgroundMethodInfluentialHIV-1 Integration Landscape during Latent and Active Infection
Cohn, L. B., da Silva, I. T., Oliveira, T. Y., Rosales, R., Parrish, E. H., Learn, G. H., Hahn, B. H., Czartoski, J., McElrath, M. J., Lehmann, C., et al. (2015) · Cell · doi:10.1016/j.cell.2015.01.020 · Cited by 460
“TG-(N)5-7-CA sequence has been associated with sites of HIV-1 integration, but an integration consensus has not been defined (Brady et al., 2009; Holman and Coffin, 2005; Lewinski et al., 2006; Serrao et al., 2014; Wang et al., 2007; Wu et al., 2005).”
BackgroundGenome-wide analysis of retroviral DNA integration
Bushman, F. D., Lewinski, M. K., Ciuffi, A., Barr, S. D., Leipzig, J. N., Hannenhalli, S. S., & Hoffmann, C. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1263 · Cited by 437
“and, in vivo , the influence of the primary DNA sequence of the target site on integration is weak, thus target-site selection is primarily not sequence-specifi”
BackgroundRetroviral DNA integration: viral and cellular determinants of target-site selection
Lewinski, M. K., Yamashita, M., Emerman, M., Ciuffi, A., Marshall, H., Crawford, G., Collins, F., Shinn, P., Leipzig, J., Hannenhalli, S., et al. (2006) · PLoS Pathogens · doi:10.1371/journal.ppat.0020060 · Cited by 364
“Previous studies showed that retroviruses have weak preferences for specific primary DNA sequences at integration sites and, when large numbers of sites are analyzed, these biases become statistically very significant [4–7].”
Metadata
- 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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