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Helitron  transposons capture and mobilize gene fragments in eukaryotes, but experimental evidence for their transposition is lacking in the absence of an isolated active element. Here we reconstruct  Helraiser , an ancient element from the bat genome, and use this transposon as an experimental tool to unravel the mechanism of  Helitron  transposition. A hairpin close to the 3′-end of the transposon functions as a transposition terminator. However, the 3′-end can be bypassed by the transposase, resulting in transduction of flanking sequences to new genomic locations.  Helraiser  transposition generates covalently closed circular intermediates, suggestive of a replicative transposition mechanism, which provides a powerful means to disseminate captured transcriptional regulatory signals across the genome. Indeed, we document the generation of novel transcripts by  Helitron  promoter capture both experimentally and by transcriptome analysis in bats. Our results provide mechanistic insight into  Helitron  transposition, and its impact on diversification of gene function by genome shuffling.

A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes