title: Guanine quadruplexes are formed by specific regions of human transposable elements.
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 evolutionarily young LINE-1 and SVA families makes these elements important contributors toward present genome-wide quadruplex distribution.
authors.forename: Matej
authors.initials: M
authors.lastname: Lexa
authors.forename: Pavlina
authors.initials: P
authors.lastname: Steflova
authors.forename: Tomas
authors.initials: T
authors.lastname: Martinek
authors.forename: Michaela
authors.initials: M
authors.lastname: Vorlickova
authors.forename: Boris
authors.initials: B
authors.lastname: Vyskot
authors.affiliation: Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic. kejnovsk@ibp.cz.
authors.forename: Eduard
authors.initials: E
authors.lastname: Kejnovsky
mesh_terms: D020087:Alu Elements; D002874:Chromosome Mapping; D004251:DNA Transposable Elements; D020077:Endogenous Retroviruses; D054856:G-Quadruplexes; D023281:Genomics; D006801:Humans; D020084:Long Interspersed Nucleotide Elements; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004251:DNA Transposable Elements