DNA transposons: nature and applications in genomics

Abstract

Repeated DNA makes up a large fraction of a typical mammalian genome, and some repetitive elements are able to move within the genome (transposons and retrotransposons). DNA transposons move from one genomic location to another by a cut-and-paste mechanism. They are powerful forces of genetic change and have played a significant role in the evolution of many genomes. As genetic tools, DNA transposons can be used to introduce a piece of foreign DNA into a genome. Indeed, they have been used for transgenesis and insertional mutagenesis in different organisms, since these elements are not generally dependent on host factors to mediate their mobility. Thus, DNA transposons are useful tools to analyze the regulatory genome, study embryonic development, identify genes and pathways implicated in disease or pathogenesis of pathogens, and even contribute to gene therapy. In this review, we will describe the nature of these elements and discuss recent advances in this field of research, as well as our evolving knowledge of the DNA transposons most widely used in these studies.

Keywords: DNA transposons; Sleeping Beauty; Tc1/mariner elements; Tol2; Transposable elements; insertional mutagenesis; piggyBac; transgenesis..

Fig. (1)

Classes of Transposable Elements (TEs). A Class I element (clade LINE-1) consist of a 5’-UTR with internal promoter activity, and two Open Reading Frames (ORFs). ORF1 encodes a nucleic acid binding protein, and ORF2 encodes a protein with Endonuclease (EN) and Reverse Transcriptase (RT) activity, lacks Long Terminal Repeats (LTR), and ends in a poly(A) tail (reviewed in [51]). Class II elements consist of a transposase gene flanked by Terminal Inverted Repeats (TIRs).

Fig. (2)

Structure of Tc1/mariner transposase. Schematic representation of the Tc1/mariner transposase, which contains a DNA-binding domain with the Helix-Turn-Helix motif (HTH), a Nuclear Localization Signal (NLS) and a catalytic domain with the DDE or DDD motif.

Fig. (3)

Transposition steps. Representation of the transposition mechanism performed by the transposase proposed for Tc1/mariner elements. The process begins with the binding of two transposase monomers to the TIRs, forming the Single-End Complex. Then, the transposon ends are brought together by both transposase monomers that form a dimer, generating the Paired-End Complex, and transposon excision takes places. Finally, the transposase dimer recognises a TA dinucleotide, joins it, and forms the Target Capture Complex to carry out the insertion.

Fig. (4)

Cut and paste reaction. Representation of cut-and-paste reaction in which the transposon is excised from one site and reintegrated at a TA target dinucleotide. Upon insertion, the TA dinucleotide is duplicated generating the Target Site Duplication (TSD). Then, the host will repair the excision site. If this repair is carried out by nonhomologous end-joining (NHEJ), a transposon footprint is generated.

Fig. (5)

Life cycle of Tc1/mariner. Shown is the evolutionary life cycle proposed for Tc1/mariner elements. The figure has been adapted from Miskey et al., [92].

Fig. (6)

DNA-Transposon System. The Transposon Vector, consisting of the DNA of interest flanked by transposon TIRs, and the Transposase Expression Vector, harbouring the transposase gene placed downstream of a strong promoter.

Fig. (7)

Gene Trap Transposons. A gene-trap designed to disrupt a gene, consisting of the transposon TIRs flanking a strong splice acceptor (SA) site followed by a reporter gene and a strong poly(A) signal. Therefore, if this transposon inserts into an intron of a gene (introns in grey; exons in blue), the inserted reporter will provoke a mis-splicing process and as a result the trapped gene is inactivated.