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Guanine quadruplexes are formed by specific regions of human transposable elements

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LEXA Matej STEFLOVA Pavlina MARTÍNEK Tomáš VORLÍČKOVÁ Michaela VYSKOT Boris KEJNOVSKÝ Eduard

Rok publikování 2014
Druh Článek v odborném periodiku
Časopis / Zdroj BMC Genomics
Fakulta / Pracoviště MU

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Citace
www http://www.biomedcentral.com/1471-2164/15/1032
Doi http://dx.doi.org/10.1186/1471-2164-15-1032
Obor Genetika a molekulární biologie
Klíčová slova G4 quadruplex; human transposable elements; circular dichroism; Bioconductor code; bioinformatics
Popis BACKGROUND: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.RESULTS:Here, 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).CONCLUSIONS:Conservation of quadruplexes at specific positions of transposable elements implies their importance in their life cycle. The increasing quadruplex presence in evolutionary young LINE-1 and SVA families makes these elements important contributors toward present genome-wide quadruplex distribution.
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