Cited by 116Virus-based gene therapy researchGenomics and Chromatin DynamicsCRISPR and Genetic Engineering

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MLV integration site selection is driven by strong enhancers and active promoters

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LaFave, Matthew C., Varshney, Gaurav K., Gildea, Derek E., Wolfsberg, Tyra G., Baxevanis, Andreas D., Burgess, Shawn M.·2014·Nucleic Acids Research

DOI 10.1093/nar/gkt1399PMC PMC3985626

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Abstract

Retroviruses integrate into the host genome in patterns specific to each virus. Understanding the causes of these patterns can provide insight into viral integration mechanisms, pathology and genome evolution, and is critical to the development of safe gene therapy vectors. We generated murine leukemia virus integrations in human HepG2 and K562 cells and subjected them to second-generation sequencing, using a DNA barcoding technique that allowed us to quantify independent integration events. We characterized >3 700 000 unique integration events in two ENCODE-characterized cell lines. We find that integrations were most highly enriched in a subset of strong enhancers and active promoters. In both cell types, approximately half the integrations were found in <2% of the genome, demonstrating genomic influences even narrower than previously believed. The integration pattern of murine leukemia virus appears to be largely driven by regions that have high enrichment for multiple marks of active chromatin; the combination of histone marks present was sufficient to explain why some strong enhancers were more prone to integration than others. The approach we used is applicable to analyzing the integration pattern of any exogenous element and could be a valuable preclinical screen to evaluate the safety of gene therapy vectors.

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SURVEY AND SUMMARY Molecular mechanisms of retroviral integration site selection
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QRIS: a machine learning framework to investigate the determinants of retroviral integration specificity
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Authors: LaFave, M. C., Varshney, G. K., Gildea, D. E., Wolfsberg, T. G., Baxevanis, A. D., & Burgess, S. M.
Affiliations: National Institutes of Health (US)
Corresponding author: Burgess, Shawn M.
ORCID: LaFave, Matthew C.
Varshney, Gaurav K.
Gildea, Derek E.
Wolfsberg, Tyra G.
Baxevanis, Andreas D.
Burgess, Shawn M.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2014-01-23
Volume: 42
Issue: 7
Pages: 4257-4269
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkt1399
PMC: PMC3985626
OpenAlex: W2034118113
Cited by: 114
References: 47
Citations by year: 2025: 3 · 2024: 8 · 2023: 8 · 2022: 6 · 2021: 8 · 2020: 5 · 2019: 14 · 2018: 9 · 2017: 10 · 2016: 20 · 2015: 15 · 2014: 8
FWCI: 11.46
Type: journal article
Language: en
Open access: gold
doi.org
Licence: public-domain
Locations: Nucleic Acids Research (publishedVersion, public-domain)
Europe PMC (PubMed Central) (publishedVersion, public-domain)
PubMed Central (publishedVersion, public-domain)
PubMed (publishedVersion)
Funders: National Institutes of Health
National Human Genome Research Institute
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
Keywords: murine leukemia virus, retroviral integration, integration site selection, enhancers, histone modifications, active chromatin, DNA barcoding, HepG2 cells, K562 cells, integration hotspots
MeSH terms: Attachment Sites, Microbiological, Enhancer Elements, Genetic, Humans, Moloney murine leukemia virus, Promoter Regions, Genetic, Virus Integration, K562 Cells, Cell Line, Tumor

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MLV integration site selection is driven by strong enhancers and active promoters

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