Molecular Reconstruction of Extinct LINE-1 Elements and Their Interaction with Nonautonomous Elements

Abstract

Non-long terminal repeat retroelements continue to impact the human genome through cis-activity of long interspersed element-1 (LINE-1 or L1) and trans-mobilization of Alu. Current activity is dominated by modern subfamilies of these elements, leaving behind an evolutionary graveyard of extinct Alu and L1 subfamilies. Because Alu is a nonautonomous element that relies on L1 to retrotranspose, there is the possibility that competition between these elements has driven selection and antagonistic coevolution between Alu and L1. Through analysis of synonymous versus nonsynonymous codon evolution across L1 subfamilies, we find that the C-terminal ORF2 cys domain experienced a dramatic increase in amino acid substitution rate in the transition from L1PA5 to L1PA4 subfamilies. This observation coincides with the previously reported rapid evolution of ORF1 during the same transition period. Ancestral Alu sequences have been previously reconstructed, as their short size and ubiquity have made it relatively easy to retrieve consensus sequences from the human genome. In contrast, creating constructs of extinct L1 copies is a more laborious task. Here, we report our efforts to recreate and evaluate the retrotransposition capabilities of two ancestral L1 elements, L1PA4 and L1PA8 that were active ∼18 and ∼40 Ma, respectively. Relative to the modern L1PA1 subfamily, we find that both elements are similarly active in a cell culture retrotransposition assay in HeLa, and both are able to efficiently trans-mobilize Alu elements from several subfamilies. Although we observe some variation in Alu subfamily retrotransposition efficiency, any coevolution that may have occurred between LINEs and SINEs is not evident from these data. Population dynamics and stochastic variation in the number of active source elements likely play an important role in individual LINE or SINE subfamily amplification. If coevolution also contributes to changing retrotransposition rates and the progression of subfamilies, cell factors are likely to play an important mediating role in changing LINE-SINE interactions over evolutionary time.

Rates and patterns of great ape retrotransposition

“…We conclude that L1 and Alu repeats have contributed minimally to gene loss by way of disrupting protein-encoding ORFs during evolution, likely because such events are deleterious and eliminated by purifying selection (42). Note, the relative number of MEI to SNP/indel gene-disruptive mutations observed between ape genomes is concordant with the ratio of disease-causing mutations reported for humans in the literature (i.e., a factor of ∼350-to 1,000-fold more SNP and indel mutations versus MEIs) (43,44).…”

“…Rates of Alu accumulation generally reciprocate those of L1s -i.e., when L1 rates are high, Alu accumulation is low (compare, for example, the orangutan and human lineage). This inverse relationship is thought to arise, in part, from the competition of SINEs and LINEs for the same reverse transcription machinery, although the effect of this interaction on the rate of insertion is both controversial and not well understood (43,44).…”

Composite non-LTR retrotransposons in hominoid primates

“…Using reconstructed L1 elements from extinct subfamilies in a present-day human cellular background, they found only limited evidence for co-evolution with Alu and considered it likely that host factors influence the interaction between the autonomous and the nonautonomous elements. 23 It will be interesting to see how efficiently L1 elements derived from different hominoids can mobilize different VNTR composites in heterologous as well as homologous cell systems. The prerequisite for such experiments is now given with the establishment of a protocol for the derivation of retrotransposition-competent induced pluripotent stem cells from non-human primate fibroblasts.…”

RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity

“…Roy-Engel's group recently recreated and evaluated the retroposition capabilities of two ancestral L1 elements, L1PA4 and L1PA8, which were active ~18 and ~40 mya, respectively [56]. Relative to the modern L1PA1 subfamily, they found that both elements were similarly active in a cell culture retroposition assay in the HeLa cell line, and both were able to efficiently trans -mobilize Alu elements from several subfamilies.…”

“…They found limited evidence of differential associations between Alu and L1 subfamilies, suggesting that other factors are likely the primary mediators of their changing interactions over evolutionary time. Population dynamics and stochastic variation in the number of active source elements likely played an important role in individual LINE or SINE subfamily amplification [56]. If coevolution also contributed to changing retroposition rates and the progression of subfamilies, cell factors were likely to play an important mediating role in changing LINE-SINE interactions over evolutionary time.…”