Gammaretroviral vector integration occurs overwhelmingly within and near DNase hypersensitive sites

Human Gene Therapy

Volumn 23, Issue 2, 2012, Pages 231-237

  Liu, Mingdong ^a   Li, Chang Long ^a,b   Stamatoyannopoulos, George ^a   Dorschner, Michael O ^a,c   Humbert, Richard ^a   Stamatoyannopoulos, John A ^a   Emery, David W ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b SICHUAN UNIVERSITY   (China)

^c KAISER PERMANENTE MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; RETROVIRUS VECTOR;

ARTICLE; CHROMATIN; CONTROLLED STUDY; DEOXYRIBONUCLEASE HYPERSENSITIVE SITE; GENE MAPPING; GENE SEQUENCE; GENOTOXICITY; HUMAN; HUMAN CELL; SARCOMA CELL; VECTOR INTEGRATION SITE; VIRUS DNA CELL DNA INTERACTION; VIRUS GENOME;

CELL LINE, TUMOR; CHROMATIN; CHROMOSOME MAPPING; DEOXYRIBONUCLEASE I; FIBROSARCOMA; GAMMARETROVIRUS; GENETIC VECTORS; HUMANS; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC; VIRUS INTEGRATION;

EID: 84863135334     PISSN: 10430342     EISSN: 15577422     Source Type: Journal    
DOI: 10.1089/hum.2010.177     Document Type: Article

References (33)

1. Adams, C.C., and Workman, J.L. (1995). Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Mol. Cell. Biol. 15, 1405-1421.
2. Aker, M., Tubb, J., Miller, D.G., et al. (2006). Integration bias of gammaretrovirus vectors following transduction and growth of primary mouse hematopoietic progenitor cells with and without selection. Mol. Ther. 14, 226-235. (Pubitemid 43942346)
3. Baum, C., Kustikova, O., Modlich, U., et al. (2006). Mutagenesis and oncogenesis by chromosomal insertion of gene transfer vectors. Hum. Gene Ther. 17, 252-263.
4. Berry, C., Hannenhalli, S., Leipzig, J., and Bushman, F.D. (2006). Selection of target sites for mobile DNA elements in the human genome. PLoS Comput. Biol. 2, e157.
5. Burgess-Beusse, B., Farrell, C., Gaszner, M., et al. (2002). The insulation of genes from external enhancers and silencing chromatin. Proc. Natl. Acad. Sci. U.S.A. 99(Suppl. 4), 16433-16437. (Pubitemid 35470990)
6. Crawford, G.E., Holt, I.E., Whittle, J., et al. (2006). Genomewide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 16, 123-131. (Pubitemid 43048941)
7. Dekker, J. (2008). Gene regulation in the third dimension. Science 319, 1793-1794. (Pubitemid 351451557)
8. Elgin, S.C. (1984). Anatomy of hypersensitive sites. Nature 309, 213-214.
9. Emery, D.W., Yannaki, E., Tubb, J., and Stamatoyannopoulos, G. (2000). A chromatin insulator protects retrovirus vectors from position effects. Proc. Natl. Acad. Sci. U. S. A. 97, 9150-9155. (Pubitemid 30626689)
10. ENCODE Project Consortium. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816.
11. Felsenfeld, G. (1996). Chromatin unfolds. Cell 86, 13-19. (Pubitemid 26256574)
12. Gross, D.S., and Garrard, W.T. (1988). Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57, 159-197.
13. Horn, S.D. (1977). Goodness-of-fit tests for discrete data: a review and an application to a health impairment scale. Biometrics 33, 237-247.
14. Jarman, A.P., and Higgs, D.R. (1988). Nuclear scaffold attachment sites in the human globin gene complexes. EMBO J. 7, 3337-3344.
15. Jin, C., Zhang, C., Wei, G., et al. (2009). H3.3/H2A.Z double variant-containing nucleosomes mare 'nucleosome-free regions' of active promoters and other regulatory regions. Nat. Genet. 41, 941-945.
16. John, S., Sabo, P.J., Thurman, R.E., et al. (2011). Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat. Genet. 43, 264-268.
17. Kieffer, L.J., Greally, J.M., Landres, I., et al. (2002). Identification of a candidate regulatory region in the human CD8 gene complex by colocalization of DNase I hypersensitive sites and matrix attachment regions which bind SATB1 and GATA-3. J. Immunol. 168, 3915-3922. (Pubitemid 34298395)
18. Kohn, D.B., Sadelain, M., Dunbar, C., et al. (2003). American Society of Gene Therapy (ASGT) ad hoc subcommittee on retroviral-mediated gene transfer to hematopoietic stem cells. Mol. Ther. 8, 180-187. (Pubitemid 37062828)
19. Lewinski, M.K., Yamashita, M., Emerman, M., et al. (2006). Retroviral DNA integration: viral and cellular determinants of target-site selection. PLoS Pathog. 2, e60.
20. Li, C.L., Xiong, D., Stamatoyannopoulos, G., and Emery, D.W. (2009). Genomic and functional assays demonstrate reduced gammaretroviral vector genotoxicity associated with use of the cHS4 chromatin insulator. Mol. Ther. 17, 716-724.
21. Lowrey, C.H., Bodine, D.M., and Nienhuis, A.W. (1992). Mechanism of DNase I hypersensitive site formation within the human globin locus control region. Proc. Natl. Acad. Sci. U. S. A. 89, 1143-1147.
22. Montini, E., Cesana, D., Schmidt, M., et al. (2006). Hematopoietic stem cell gene transfer in a tumor-prone mouse model uncovers low genotoxicity of lentiviral vector integration. Nat. Biotechnol. 24, 687-696. (Pubitemid 43882120)
23. Rasheed, S., Nelson-Rees, W.A., Toth, E.M., et al. (1974). Characterization of a newly derived human sarcoma cell line (HT-1080). Cancer 33, 1027-1033.
24. Reitman, M., Lee, E., Westphal, H., and Felsenfeld, G. (1993). An enhancer/locus control region is not sufficient to open chromatin. Mol. Cell. Biol. 13, 3990-3998. (Pubitemid 23187627)
25. Rohdewohld, H., Weiher, H., Reik, W., et al. (1987). Retrovirus integration and chromatin structure: Moloney murine leukemia proviral integration sites map near DNase I-hypersensitive sites. J. Virol. 61, 336-343. (Pubitemid 17001729)
26. Sabo, P.J., Hawrylycz, M., Wallace, J.C., et al. (2004). Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc. Natl. Acad. Sci. U. S. A. 101, 16837-16842. (Pubitemid 39601325)
27. Sabo, P.J., Kuehn, M.S., Thurman, R., et al. (2006). Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat. Methods 3, 511-518. (Pubitemid 43941768)
28. Sekimata, M., Perez-Melgosa, M., Miller, S.A., et al. (2009). CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus. Immunity 31, 551-564.
29. Vijaya, S., Steffen, D.L., and Robinson, H.L. (1986). Acceptor sites for retroviral integrations map near DNase I-hypersensitive sites in chromatin. J. Virol. 60, 683-692. (Pubitemid 17174911)
30. Wu, C. (1980). The 5¢ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286, 854-860. (Pubitemid 10010150)
31. Wu, X., Li, Y., Crise, B., and Burgess, S.M. (2003). Transcription start sites in the human genome are favored sites for MLV integration. Science 300, 1749-1751. (Pubitemid 36712571)
32. Zhang, Y., Strissel, P., Strick, R., et al. (2002). Genomic DNA breakpoints in AML1/RUNX1 and ETO cluster with topoisomerase II DNA cleavage and DNase I hypersensitive sites in t(8;21) leukemia. Proc. Natl. Acad. Sci. U. S. A. 99, 3070-3075. (Pubitemid 34240587)
33. Zhao, Z., Tavoosidana, G., Sjolinder, M., et al. (2006). Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions. Nat. Genet. 38, 1341-1347. (Pubitemid 44646299)