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Non-LTR retrotransposons insert into eukaryotic genomes by target-primed reverse transcription (TPRT), a process in which cleaved DNA targets are used to prime reverse transcription of the element's RNA transcript. Many of the steps in the integration pathway of these elements can be characterized in vitro for the R2 element because of the rigid sequence specificity of R2 for both its DNA target and its RNA template. R2 retrotransposition involves identical subunits of the R2 protein bound to different DNA sequences upstream and downstream of the insertion site. The key determinant regulating which DNA-binding conformation the protein adopts was found to be a 320-nt RNA sequence from near the 5′ end of the R2 element. In the absence of this 5′ RNA the R2 protein binds DNA sequences upstream of the insertion site, cleaves the first DNA strand, and conducts TPRT when RNA containing the 3′ untranslated region of the R2 transcript is present. In the presence of the 320-nt 5′ RNA, the R2 protein binds DNA sequences downstream of the insertion site. Cleavage of the second DNA strand by the downstream subunit does not appear to occur until after the 5′ RNA is removed from this subunit. We postulate that the removal of the 5′ RNA normally occurs during reverse transcription, and thus provides a critical temporal link to first- and second-strand DNA cleavage in the R2 retrotransposition reaction. [ABSTRACT FROM AUTHOR]

Linear chromosomes shorten in every round of replication. In Drosophila, telomere‐specialized long interspersed retrotransposable elements (LINEs) belonging to the jockey clade offset this shortening by forming head‐to‐tail arrays at Drosophila telomere ends. As such, these telomeric LINEs have been considered adaptive symbionts of the genome, protecting it from premature decay, particularly as Drosophila lacks a conventional telomerase holoenzyme. However, as reviewed here, recent work reveals a high degree of variation and turnover in the telomere‐specialized LINE lineages across Drosophila. There appears to be no absolute requirement for LINE activity to maintain telomeres in flies, hence the suggestion that the telomere‐specialized LINEs may instead be neutral or in conflict with the host, rather than adaptive. [ABSTRACT FROM AUTHOR]

The analyses of gene duplications by retroposition have revealed an excess of male-biased duplicates generated from X chromosome to autosomes in flies and mammals. Investigating these genes is of primary importance in understanding sexual dimorphism and genome evolution. In a particular instance in Drosophila, X-linked nuclear transport genes (Ntf-2 and ran) have given rise to autosomal retroposed copies three independent times (along the lineages leading to Drosophila melanogaster, D. ananassae, and D. grimshawi). Here we explore in further detail the expression and the mode of evolution of these Drosophila Ntf-2- and ran-derived retrogenes. Five of the six retrogenes show male-biased expression. The ran-like gene of D. melanogaster and D. simulans has undergone recurrent positive selection. Similarly, in D. ananassae and D. atripex, the Ntf-2 and ran retrogenes show evidence of past positive selection. The data suggest that strong selection is acting on the origin and evolution of these retrogenes. Avoiding male meiotic X inactivation, increasing level of expression of X-linked genes in male testes, and/or sexual antagonism might explain the recurrent duplication of retrogenes from X to autosomes. Interestingly, the ran-like in D. yakuba has mostly pseudogenized alleles. Disablement of the ran-like gene in D. yakuba indicates turnover of these duplicates. We discuss the possibility that Dntf-2r and ran-like might be involved in genomic conflicts during spermatogenesis. [ABSTRACT FROM AUTHOR]