Abstract
Chicken repeat 1 (CR1) retroposons are the most abundant superfamily of transposable elements in the genomes of birds, crocodilians, and turtles. However, CR1 mobilization remains poorly understood. In this article, I document that the diverse CR1 lineages of land vertebrates share a highly conserved hairpin structure and an octamer microsatellite motif at their very 3′ ends. Together with the presence of these same motifs in the tails of CR1-mobilized short interspersed elements, this suggests that the minimum requirement for CR1 transcript recognition and retrotransposition is a complex >50-nt structure. Such a highly specific recognition sequence readily explains why CR1-dominated genomes generally contain very few retrogenes. Conversely, the mammalian richness in retrogenes results from CR1 extinction in their early evolution and subsequent establishment of L1 dominance.
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The author thanks Aurélie Kapusta and Regine Jahn for critical reading of this manuscript.
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239_2015_9692_MOESM1_ESM.pdf
Figure S1. Predicted secondary RNA structure of the 3′ hairpin required for CR1 retrotransposition. The elements were analyzed in mfold (Zuker 2003) and correspond to the examples for CR1 (PSLINE) and co-mobilized SINEs (CryI, CryIIB) shown in Fig. 1d. Supplementary material 1 (PDF 441 kb)
239_2015_9692_MOESM2_ESM.pdf
Table S1. Structural elements in the 3' ends of 117 CR1 subfamilies from land vertebrates. Supplementary material 2 (PDF 63 kb)
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Suh, A. The Specific Requirements for CR1 Retrotransposition Explain the Scarcity of Retrogenes in Birds. J Mol Evol 81, 18–20 (2015). https://doi.org/10.1007/s00239-015-9692-x
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DOI: https://doi.org/10.1007/s00239-015-9692-x