Transposable elements (TEs) are repetitive sequences found in nearly every eukaryotic species and contribute to a large proportion of the genome in many species. Accurate characterization and categorization of repetitive elements in a genome can be challenging, sometimes significant underestimated in early attempts even in sequenced genomes and previously undiscovered elements continue to emerge. For example, the Drosophila melanogaster genome was thought to contain 6-8% TEs, it was soon revised to ~22% [1–3]. Human genome was believed to contain about ~50% repeats, a recent study suggested that they may contribute up to two thirds of the genome .
In addition to the fundamental knowledge brought about by research on TEs, the disruptive forces of TEs can be harnessed and utilized to benefit scientific research and technology development. These TE derived tools fall into different application categories. TEs can be used to create stable transgenic organisms that are essential for studies on insertional mutagenesis, enhancer trapping and gene trapping . Due to their disruptive nature, TEs are capable of inserting into multiple sites of a gene, creating a series of TE tagged mutation lines . Different insertional mutant lines may have different levels of severity in terms of phenotypic changes. DNA-type elements are unstable and their excision from an insertional mutant line may restore expression of the disrupted genes, resulting in reversion from mutant phenotypes. These revertant lines provide support for the causative genotype for a phenotype . The target genes in TE tagged lines can be cloned based on the TE tag sequences, a major advantage over the random point mutagenesis approaches (e.g. EMS and UV mediated mutation). Development of this technology for a wide range of hosts requires deep understanding of transposition mechanisms of a variety of elements. The abundance of TEs in most large genomes also make them candidates as genetic markers [8, 9]. Gene therapy to treat genetic diseases and cancers using viral vectors encountered significant challenges due to immune response to the viral vectors [10, 11], leading researchers to consider DNA transposons for alternative vectors . It has also been demonstrated that PiggyBac transposons can be used to create marker free induced pluripotency stem cells . Genetic control of pest insect population traditionally uses radiation for mass production of sterile male insects. With the insect transformation technology to create transgenic insects bearing genes that can be used for their control, transposons gained much attention to be potential gene drive vectors to spread transgenes among pest populations to achieve genetic control .
Yellow fever mosquito, Aedes aegypti, is a vector for Yellow Fever, Dengue and Chikungunia virus. Large scale mosquito control has been proven a challenging task. Recently, using biotechnology in mosquito control such as Oxitec has garnered much attention and is currently under pilot test . In this approach, a large number of transgenic male mosquitoes are released to outcompete wild male mosquitoes to mate with female mosquitoes. The transgene causes larva lethality in the next generation. To achieve continuous control effect, a massive number of mosquitoes need to be released on a regular basis. In addition, the ecological consequences, due to the changed mosquito population size and structure, remain a concern. Therefore, cost efficient approaches that introduce minimal alteration of the ecosystem are desirable. One attractive approach is population replacement where a small number of transgenic mosquitoes resistant to pathogens can spread the transgenes to the wild population, pushing the defense line beyond the disease vectors. A critical factor in this approach relies on a gene drive system to spread transgenes. Transposons can increase their frequency in a population, therefore are considered good candidates for a gene drive system . Transgenic mosquitoes resistant to pathogens such as Dengue virus and Plasmodium falciparum have been established [16, 17]. However, the commonly used transposons for insect transgenesis rarely remobilize efficiently once they integrate into the mosquito chromosomes [18–22]. Therefore, endogenous active transposon elements in the mosquito genome may provide a much needed tool.
TEs comprise 47% of the genome of Aedes aegypti, a rich source of materials to search for active TEs. TEfam, a database dedicated for vector insects, contains a total of 1089 A. aetypti TE families, 826 characterized as retro element families and 247 DNA element families. Many of these families are non-autonomous elements that depend on their autonomous partners to provide transposase for their mobilization. For example there are 143 MITE families that account for about 16% of the total genome sequences . The availability of these TE sequences provides an opportunity to identify candidates for active endogenous TEs in the yellow fever mosquito genome. Previous reverse genetic approaches for active TE discovery suggested that the presence of multiple identical copies of an element is a flashing indicator for current or very recent transposition activity [24, 25].
In this study, genome wide analyses were performed to identify elements with multiple identical copies inserted at difference loci. Further analysis of the best candidates for active transposons led to the identification and characterization of 26 families (~6000 copies) of novel transposable elements designated as ATons. These elements are non-autonomous bearing terminal inverted repeats and insert specifically at dinucleotide “AT”, a feature not seen in known TE superfamilies. The autonomous elements for ATons remain mysterious despite exhaustive genome wide database searches.