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. 2019 Nov 25;11(12):3382–3392. doi: 10.1093/gbe/evz255

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© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Fig. 2. — —Schematic representation of discontinuous reverse-transcription and recombination steps. (A) Two members of a LTR retrotransposon clan are transcriptionally activated and the corresponding genomic RNA (gRNA) progenitors (starting and ending in the R regions of 5′- and 3′-LTR, respectively) are copackaged. (B) Reverse-transcriptase/RNaseH activity (RT/R, green) is primed by tRNA annealing the priming-binding-site (pbs) of gRNA1 (orange), and minus-single-strand extrachromosomal cDNA ((-)ss-ecDNA) is synthesized. (C) First strand transfer: strong-stop (-)ss-ecDNA transfers to a second gRNA2 (green) (first recombinogenic step; the hypothesized recombination point is marked with an inverted gray triangle), using sequence homologies in the R region (marked with a dotted box). (D) At the same time that RNAseH activity proceeds (not shown), the (-)ss-ecDNA is extended using gRNAs as alternate templates (second recombinogenic step; a single hypothesized recombination point is marked with an inverted black triangle, but note that more than one event is possible). The color-coded newly synthesized (-)ss-ecDNA molecule is represented as a mosaic of the two progenitor gRNAs. Although RNAseH activity degrades portions of gRNA2 template (not shown), priming of poly-purine-track (ppt) allows nascent plus-single-strand extrachromosomal cDNA ((+)ss-ecDNA) synthesis until the end of the (-)ss-ecDNA molecule used as template. (E) Second strand transfer: strong-stop (+)ss-ecDNA swaps toward the 5′ area of the (-)ss-ecDNA. In addition, RT/R final extensions take place. (F) After final extensions, a mosaic blunt-ended linear extrachromosomal DNA (ds-ecDNA) molecule with two identical LTRs is generated. U3/R/U5, domains within LTRs; GAG, structural protein; POL, polyprotein.