Abstract
BackgroundTransposable elements form a significant proportion of eukaryotic genomes. Recently, Lexa et al. (Nucleic Acids Res 42:968-978, 2014) reported that plant long terminal repeat (LTR) retrotransposons often contain potential quadruplex sequences (PQSs) in their LTRs and experimentally confirmed their ability to adopt four-stranded DNA conformations.ResultsHere, we searched for PQSs in human retrotransposons and found that PQSs are specifically localized in the 3’-UTR of LINE-1 elements, in LTRs of HERV elements and are strongly accumulated in specific regions of SVA elements. Circular dichroism spectroscopy confirmed that most PQSs had adopted monomolecular or bimolecular guanine quadruplex structures. Evolutionarily young SVA elements contained more PQSs than older elements and their propensity to form quadruplex DNA was higher. Full-length L1 elements contained more PQSs than truncated elements; the highest proportion of PQSs was found inside transpositionally active L1 elements (PA2 and HS families).ConclusionsConservation of quadruplexes at specific positions of transposable elements implies their importance in their life cycle. The increasing quadruplex presence in evolutionarily young LINE-1 and SVA families makes these elements important contributors toward present genome-wide quadruplex distribution.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1032) contains supplementary material, which is available to authorized users.
Highlights
Transposable elements form a significant proportion of eukaryotic genomes
Potential quadruplex-forming sequences are located in specific regions of human transposable elements We analyzed the localization of potential quadruplex sequences (PQSs) inside main groups of human transposable elements (TEs), namely in LINE-1, Alu elements, HERV retrotransposons and SVA elements
The overall highest abundance of PQSs was observed in SVA (PQS was in 36.2% of elements) followed by LINE-1 (PQS in 7.7% of elements) and HERV elements (PQS in 4.8% of elements)
Summary
Transposable elements form a significant proportion of eukaryotic genomes. Recently, Lexa et al (Nucleic Acids Res 42:968-978, 2014) reported that plant long terminal repeat (LTR) retrotransposons often contain potential quadruplex sequences (PQSs) in their LTRs and experimentally confirmed their ability to adopt four-stranded DNA conformations. Transposable elements (TEs) are abundant inhabitants of eukaryotic genomes, representing e.g. about 50% of the human genome and up to 90% in some plant species. During the last two decades, it became widely accepted that TEs, as an inherently dynamic genome component, Human LTR retrotransposons are represented by endogenous retroviruses (HERV) but their activity is currently very limited: most HERVs were inserted into the genomes of our ancestors earlier that 25 mya [11]. The majority of human TEs result from the present and past activity of non-LTR retrotransposons, including the LINE-1, Alu and SVA elements [8]. Alus were active over the past 65 mya and the human genome contains more than 1 million copies. Both Alu and SVA are trans-mobilized by the L1 machinery [14]
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