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Background  The Drosophila INterspersed Elements-1 ( DINE-1/INE1 ) transposable elements (TEs) are the most abundant component of the  Drosophila melanogaster  genome and have been associated with functional gene duplications.  DINE-1  TEs do not encode any proteins (non-autonomous) thus are moved by autonomous partners. The identity of the autonomous partners has been a mystery. They have been allied to  Helitrons  (rolling-circle transposons), MITEs (DNA transposons), and non-LTR retrotransposons by different authors.    Results  We report multiple lines of bioinformatic evidence that illustrate the relationship of  DINE-1  like TEs to endonuclease-encoding rolling-circle TEs ( Helentrons ). The structural features of  Helentrons  are described, which resemble the organization of the non-autonomous partners, but differ significantly from canonical  Helitrons . In addition to the presence of an endonuclease domain fused to the Rep/Helicase protein,  Helentrons  have distinct structural features. Evidence is presented that illustrates that  Helentrons  are widely distributed in invertebrate, fish, and fungal genomes. We describe an intermediate family from the  Phytophthora infestans  genome that phylogenetically groups with  Helentrons  but that displays  Helitron  structure. In addition, evidence is presented that  Helentrons  can capture gene fragments in a pattern reminiscent of canonical  Helitrons .    Conclusions  We illustrate the relationship of  DINE-1  and related TE families to autonomous partners, the  Helentrons . These findings will allow their proper classification and enable a more accurate understanding of the contribution of rolling-circle transposition to the birth of new genes, gene networks, and genome composition.

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DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons)