Common physical properties of DNA affecting target site selection of Sleeping Beauty and other Tc1/mariner transposable elements

Thomas J. Vigdal, Christopher D. Kaufman, Zsuzsanna Izsvák, Daniel F. Voytas, Zoltán Ivics

Research output: Contribution to journalArticlepeer-review

208 Scopus citations

Abstract

Sleeping Beauty (SB) is the most active Tc1/mariner-type transposable element in vertebrates, and is therefore a valuable vector for transposon mutagenesis in vertebrate models and for human gene therapy. We have analyzed factors affecting target site selection of SB in mammalian cells, by generating transposition events from extrachromosomal plasmids to chromosomes. In contrast to the local hopping observed when transposition is induced from a chromosomal context, mapping of 138 unique SB insertions on human chromosomes showed a fairly random genomic distribution, and a 35% occurrence of transposition into genes. Inspection of the DNA flanking the sites of element integration revealed significant differences from random DNA in both primary sequence and physical properties. The consensus sequence of SB target sites was found to be a palindromic AT-repeat, ATATATAT, in which the central TA is the canonical target site. We found however, that target site selection is determined primarily on the level of DNA structure, and not by specific base-pair interactions. Computational analyses revealed that insertion sites tend to have a bendable structure and a palindromic pattern of potential hydrogen-bonding sites in the major groove of the DNA. These features appear conserved in the Tc1/mariner family of transposons and in other, distantly related elements that share a common catalytic domain of the transposase, and integrate fairly randomly. No similar target site preference was found for non-randomly integrating elements. Our results suggest common factors influencing target site selection of a wide range of transposable elements.

Original languageEnglish (US)
Pages (from-to)441-452
Number of pages12
JournalJournal of Molecular Biology
Volume323
Issue number3
DOIs
StatePublished - 2002

Bibliographical note

Funding Information:
We thank D. Fiedler & E. Stüwe for their technical assistance, members of the Transposition Group at the MDC and Ericka Havecker for their helpful comments on the manuscript, and Dr I. Bruckner for helpful discussions on the DNase I assay. The HBondView and DNA structure analysis softwares were kind gifts from G. C. Liao. This work was supported by EU grant QLG2-CT-2000-00821.

Keywords

  • Bendability
  • Hydrogen bond
  • Target site
  • Transposition
  • Transposon

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