New software helps to find out why “jumping genes” are activated

The new tool PoPoolationTE2 allows for calculating the frequency in Pool-Seq reactions. (Figure: RobertKofler/Vetmeduni Vienna

transposable elements

Jumping genes, so-called transposons, reproduce as parasites in the genome. This selfish behaviour can be an evolutionary advantage for the organism or harm it. There is still a debate about the factors controlling the activity of transposons. Comparisons between populations could shed an answer on this but have been biased due to technical problems so far. The software PoPoolationTE2 developed by the Institute of Population Genetics at the University of Veterinary Medicine, Vienna enables an unbiased analysis for the first time and determines the frequency of transposons. This might also be useful for cancer research and neurology. The software was presented in the renowned journals Molecular Biology and Evolution.

The genome is not a fixed code but flexible. It allows changes in the genes. Transposons, however, so-called jumping genes, interpret this flexibility in a much freer way than “normal” genes. They reproduce in the genome and chose their position themselves. Transposons can also jump into a gene and render it inoperative. Thus, they are an important distinguishing mark for the development of different organisms.

Unclear what triggers transposon activity

However, it is still unclear how jumping genes developed and what influences their activity. “In order to find out how, for instance, climate zones influence activity, we must be able to compare the frequency of transposons in different populations – in different groups of individuals,” explained bioinformatician Robert Kofler from the Institute of Population Genetics at the University of Veterinary Medicine, Vienna. But this frequency has not yet been determined precisely.

New software for a low-priced method

Transposons are detected by DNA sequencing. But this detection cannot be carried out for every single member of a population. “At the moment, this would go beyond the available resources regarding finance and amount of work. The only – and much cheaper – option is to analyse an entire population in one reaction,” explained last author and head of the Institute pf Population Genetics of the Vetmeduni Vienna Christian Schlötterer. This method, which Schlötterer has established using the example of fruit flies, is called Pool-Seq. It is also routinely applied to detect transposons. Existing analysis programmes, however, could not provide a precise result in this case. So far, each analysis has been biased by different factors such as the sequencing depth and the distance between paired reads.

For this purpose, Kofler developed the new software PoPoolationTE2. “If we sequence entire populations, each reaction provides a different result. The number of mixed individuals is always the same, but the single individuals differ,” explained Kofler. Furthermore, technical differences in the sample processing, among others, have influenced the analysis so far. PoPoolationTE2 is not affected by these factors. Thus, questions about the activity of transposons can be answered precisely for Pool-Seq reactions.

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