Publication Details

Guanine quadruplexes are formed by specific regions of human transposable elements

LEXA, M.; ŠTEFLOVÁ, P.; MARTÍNEK, T.; VORLÍČKOVÁ, M.; VYSKOT, B.; KEJNOVSKÝ, E. Guanine quadruplexes are formed by specific regions of human transposable elements. BMC GENOMICS, 2014, vol. 15, no. 1032, p. 1-12. ISSN: 1471-2164.
Czech title
Guaninové kvadruplexy jsou formovány specifickými regiony lidských transponovatelných elementů
Type
journal article
Language
English
Authors
Lexa Matej, Ing., Ph.D. (DFIT-Dean)
Šteflová Pavlína (FIT)
Martínek Tomáš, doc. Ing., Ph.D. (DCSY)
Vorlíčková Michaela, prof. RNDr., DrSc.
Vyskot Boris, prof. RNDr., DrSc.
Kejnovský Eduard, doc. RNDr., CSc.
URL
Keywords

G4 quadruplex; human transposable elements; circular dichroism; Bioconductor code; bioinformatics

Abstract

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.

Published
2014
Pages
1–12
Journal
BMC GENOMICS, vol. 15, no. 1032, ISSN 1471-2164
DOI
10.1186/1471-2164-15-1032
UT WoS
000355992300001
EID Scopus
2-s2.0-84928238522
BibTeX 
@article{BUT119812,
  author="Matej {Lexa} and Pavlína {Šteflová} and Tomáš {Martínek} and Michaela {Vorlíčková} and Boris {Vyskot} and Eduard {Kejnovský}",
  title="Guanine quadruplexes are formed by specific regions of human transposable elements",
  journal="BMC GENOMICS",
  year="2014",
  volume="15",
  number="1032",
  pages="1--12",
  doi="10.1186/1471-2164-15-1032",
  issn="1471-2164",
  url="http://www.biomedcentral.com/1471-2164/15/1032"
}
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