This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Yant, S. R.
Right arrow Articles by Kay, M. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yant, S. R.
Right arrow Articles by Kay, M. A.

 Previous Article  |  Next Article 

Molecular and Cellular Biology, March 2005, p. 2085-2094, Vol. 25, No. 6
0270-7306/05/$08.00+0     doi:10.1128/MCB.25.6.2085-2094.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

High-Resolution Genome-Wide Mapping of Transposon Integration in Mammals

Stephen R. Yant,1 Xiaolin Wu,2 Yong Huang,1 Brian Garrison,1 Shawn M. Burgess,3 and Mark A. Kay1*

Departments of Pediatrics and Genetics, Stanford University School of Medicine, Stanford, California,1 Laboratory of Molecular Technology, SAIC—Frederick, National Cancer Institute—Frederick, Frederick,2 Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland3

Received 8 October 2004/ Returned for modification 15 November 2004/ Accepted 15 December 2004

The Sleeping Beauty (SB) transposon is an emerging tool for transgenesis, gene discovery, and therapeutic gene delivery in mammals. Here we studied 1,336 SB insertions in primary and cultured mammalian cells in order to better understand its target site preferences. We report that, although widely distributed, SB integration recurrently targets certain genomic regions and shows a small but significant bias toward genes and their upstream regulatory sequences. Compared to those of most integrating viruses, however, the regional preferences associated with SB-mediated integration were much less pronounced and were not significantly influenced by transcriptional activity. Insertions were also distinctly nonrandom with respect to intergenic sequences, including a strong bias toward microsatellite repeats, which are predominantly enriched in noncoding DNA. Although we detected a consensus sequence consistent with a twofold dyad symmetry at the target site, the most widely used sites did not match this consensus. In conjunction with an observed SB integration preference for bent DNA, these results suggest that physical properties may be the major determining factor in SB target site selection. These findings provide basic insights into the transposition process and reveal important distinctions between transposon- and virus-based integrating vectors.

* Corresponding author. Mailing address: Stanford University School of Medicine, Department of Pediatrics, 300 Pasteur Dr., Room G-305, Stanford, CA 94305-5208. Phone: (650) 498-6531. Fax: (650) 498-6540. E-mail: markay{at}stanford.edu.

Molecular and Cellular Biology, March 2005, p. 2085-2094, Vol. 25, No. 6
0022-538X/05/$08.00+0     doi:10.1128/MCB.25.6.2085-2094.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Starr, T. K., Allaei, R., Silverstein, K. A. T., Staggs, R. A., Sarver, A. L., Bergemann, T. L., Gupta, M., O'Sullivan, M. G., Matise, I., Dupuy, A. J., Collier, L. S., Powers, S., Oberg, A. L., Asmann, Y. W., Thibodeau, S. N., Tessarollo, L., Copeland, N. G., Jenkins, N. A., Cormier, R. T., Largaespada, D. A. (2009). A Transposon-Based Genetic Screen in Mice Identifies Genes Altered in Colorectal Cancer. Science 323: 1747-1750 [Abstract] [Full Text]  
  • Clark, K. J., Carlson, D. F., Leaver, M. J., Foster, L. K., Fahrenkrug, S. C. (2009). Passport, a native Tc1 transposon from flatfish, is functionally active in vertebrate cells. Nucleic Acids Res 37: 1239-1247 [Abstract] [Full Text]  
  • Paatero, A. O., Turakainen, H., Happonen, L. J., Olsson, C., Palomaki, T., Pajunen, M. I., Meng, X., Otonkoski, T., Tuuri, T., Berry, C., Malani, N., Frilander, M. J., Bushman, F. D., Savilahti, H. (2008). Bacteriophage Mu integration in yeast and mammalian genomes. Nucleic Acids Res 36: e148-e148 [Abstract] [Full Text]  
  • Linheiro, R. S., Bergman, C. M. (2008). Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element. Nucleic Acids Res 36: 6199-6208 [Abstract] [Full Text]  
  • Labrador, M., Sha, K., Li, A., Corces, V. G. (2008). Insulator and Ovo Proteins Determine the Frequency and Specificity of Insertion of the gypsy Retrotransposon in Drosophila melanogaster. Genetics 180: 1367-1378 [Abstract] [Full Text]  
  • Garrison, B. S., Yant, S. R., Mikkelsen, J. G., Kay, M. A. (2007). Postintegrative Gene Silencing within the Sleeping Beauty Transposition System. Mol. Cell. Biol. 27: 8824-8833 [Abstract] [Full Text]  
  • Wilber, A., Linehan, J. L., Tian, X., Woll, P. S., Morris, J. K., Belur, L. R., McIvor, R. S., Kaufman, D. S. (2007). Efficient and Stable Transgene Expression in Human Embryonic Stem Cells Using Transposon-Mediated Gene Transfer. Stem Cells 25: 2919-2927 [Abstract] [Full Text]  
  • Cadinanos, J., Bradley, A. (2007). Generation of an inducible and optimized piggyBac transposon system. Nucleic Acids Res 0: gkm446v1-8 [Abstract] [Full Text]  
  • Yant, S. R., Huang, Y., Akache, B., Kay, M. A. (2007). Site-directed transposon integration in human cells. Nucleic Acids Res 35: e50-e50 [Abstract] [Full Text]  
  • Dunbar, C. E. (2007). The Yin and Yang of Stem Cell Gene Therapy: Insights into Hematopoiesis, Leukemogenesis, and Gene Therapy Safety. ASH Education Book 2007: 460-465 [Abstract] [Full Text]  
  • Liu, L., Liu, H., Visner, G., Fletcher, B. S. (2006). Sleeping Beauty-mediated eNOS gene therapy attenuates monocrotaline-induced pulmonary hypertension in rats. FASEB J. 20: 2594-2596 [Abstract] [Full Text]  
  • Liu, H., Liu, L., Fletcher, B. S., Visner, G. A. (2006). Sleeping Beauty-based gene therapy with indoleamine 2,3-dioxygenase inhibits lung allograft fibrosis. FASEB J. 20: 2384-2386 [Abstract] [Full Text]  
  • Wu, S. C.-Y., Meir, Y.-J. J., Coates, C. J., Handler, A. M., Pelczar, P., Moisyadi, S., Kaminski, J. M. (2006). From the Cover: piggyBac is a flexible and highly active transposon as compared to Sleeping Beauty, Tol2, and Mos1 in mammalian cells. Proc. Natl. Acad. Sci. USA 103: 15008-15013 [Abstract] [Full Text]  
  • Maragathavally, K. J., Kaminski, J. M., Coates, C. J. (2006). Chimeric Mos1 and piggyBac transposases result in site-directed integration. FASEB J. 20: 1880-1882 [Abstract] [Full Text]  
  • Babushok, D. V., Ostertag, E. M., Courtney, C. E., Choi, J. M., Kazazian, H. H. Jr. (2006). L1 integration in a transgenic mouse model. Genome Res 16: 240-250 [Abstract] [Full Text]  
  • Huang, X., Wilber, A. C., Bao, L., Tuong, D., Tolar, J., Orchard, P. J., Levine, B. L., June, C. H., McIvor, R. S., Blazar, B. R., Zhou, X. (2006). Stable gene transfer and expression in human primary T cells by the Sleeping Beauty transposon system. Blood 107: 483-491 [Abstract] [Full Text]  
  • Geurts, A. M., Hackett, C. S., Bell, J. B., Bergemann, T. L., Collier, L. S., Carlson, C. M., Largaespada, D. A., Hackett, P. B. (2006). Structure-based prediction of insertion-site preferences of transposons into chromosomes.. Nucleic Acids Res 34: 2803-2811 [Abstract] [Full Text]  
  • Collier, L. S., Largaespada, D. A. (2005). Hopping around the Tumor Genome: Transposons for Cancer Gene Discovery. Cancer Res. 65: 9607-9610 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»