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Open Access Research article

Genome-wide target profiling of piggyBac and Tol2 in HEK 293: pros and cons for gene discovery and gene therapy

Yaa-Jyuhn J Meir1*, Matthew T Weirauch2, Herng-Shing Yang3, Pei-Cheng Chung4, Robert K Yu5 and Sareina C-Y Wu4*

Author Affiliations

1 Department of Biomedical Sciences, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Tao-Yuan 333, Taiwan

2 Banting and Best Department of Medical Research and Donnelly Centre for Cellular and Biomolecular Research University of Toronto, 112 College Street, Toronto, Ontario, M5 S 3E1, Canada

3 YongKang Veterans Hospital, 427 Fuxing Road, Yongkang City, Tainan 71051, Taiwan

4 Molecular Medicine Research Center, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Tao-Yuan 333, Taiwan

5 Institute of Molecular Medicine and Genetics and Institute of Neuroscience, Georgia Health Sciences University, 1120 15th Street, Augusta, Georgia 30912, USA

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BMC Biotechnology 2011, 11:28  doi:10.1186/1472-6750-11-28

Published: 30 March 2011



DNA transposons have emerged as indispensible tools for manipulating vertebrate genomes with applications ranging from insertional mutagenesis and transgenesis to gene therapy. To fully explore the potential of two highly active DNA transposons, piggyBac and Tol2, as mammalian genetic tools, we have conducted a side-by-side comparison of the two transposon systems in the same setting to evaluate their advantages and disadvantages for use in gene therapy and gene discovery.


We have observed that (1) the Tol2 transposase (but not piggyBac) is highly sensitive to molecular engineering; (2) the piggyBac donor with only the 40 bp 3'-and 67 bp 5'-terminal repeat domain is sufficient for effective transposition; and (3) a small amount of piggyBac transposases results in robust transposition suggesting the piggyBac transpospase is highly active. Performing genome-wide target profiling on data sets obtained by retrieving chromosomal targeting sequences from individual clones, we have identified several piggyBac and Tol2 hotspots and observed that (4) piggyBac and Tol2 display a clear difference in targeting preferences in the human genome. Finally, we have observed that (5) only sites with a particular sequence context can be targeted by either piggyBac or Tol2.


The non-overlapping targeting preference of piggyBac and Tol2 makes them complementary research tools for manipulating mammalian genomes. PiggyBac is the most promising transposon-based vector system for achieving site-specific targeting of therapeutic genes due to the flexibility of its transposase for being molecularly engineered. Insights from this study will provide a basis for engineering piggyBac transposases to achieve site-specific therapeutic gene targeting.