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Genome-wide analysis of transposon and retroviral insertions reveals preferential integrations in regions of DNA flexibility
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Vrljicak, P., Tao, S., Varshney, G. K., Quach, H. N. B., Joshi, A., LaFave, M. C., Burgess, S. M. and Sampath, Karuna (2016) Genome-wide analysis of transposon and retroviral insertions reveals preferential integrations in regions of DNA flexibility. G3 : Genes Genomes Genetics, 6 (4). pp. 805-817. doi:10.1534/g3.115.026849 ISSN 2160-1836.
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Official URL: http://dx.doi.org/10.1534/g3.115.026849
Abstract
DNA transposons and retroviruses are important transgenic tools for genome engineering. An important consideration affecting the choice of transgenic vector is their insertion site preferences. Previous large-scale analyses of Ds transposon integration sites in plants were done on the basis of reporter gene expression or germline transmission, making it difficult to discern vertebrate integration preferences. Here, we compare over 1300 Ds transposon integration sites in zebrafish, with Tol2 transposon and retroviral integration sites. Genome-wide analysis shows that Ds integration sites in the presence or absence of marker selection are remarkably similar and distributed throughout the genome. No strict motif was found, but a preference for structural features in the target DNA associated with DNA flexibility (Twist, Tilt, Rise, Roll, Shift and Slide) was observed. Remarkably, this feature is also found in transposon and retroviral integrations in maize and mouse cells. Our findings show that structural features influence integration of heterologous DNA in genomes, and have implications for targeted genome engineering.
| Item Type: | Journal Article | ||||||||
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| Subjects: | Q Science > QH Natural history > QH426 Genetics | ||||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Cell & Developmental Biology Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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| Library of Congress Subject Headings (LCSH): | Transposons, Genomes, Gene targeting, Functional genomics, Retroviruses , Mice, Embryonic stem cells, Zebra danio | ||||||||
| Journal or Publication Title: | G3 : Genes Genomes Genetics | ||||||||
| Publisher: | Genetics Society of America | ||||||||
| ISSN: | 2160-1836 | ||||||||
| Official Date: | 27 January 2016 | ||||||||
| Dates: |
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| Volume: | 6 | ||||||||
| Number: | 4 | ||||||||
| Page Range: | pp. 805-817 | ||||||||
| DOI: | 10.1534/g3.115.026849 | ||||||||
| Status: | Peer Reviewed | ||||||||
| Publication Status: | Published | ||||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||||
| Date of first compliant deposit: | 30 June 2016 | ||||||||
| Date of first compliant Open Access: | 30 June 2016 | ||||||||
| Funder: | Warwick Medical School, National Institutes of Health (U.S.) (NIH) |
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