LEXA, Matej, Pavlina STEFLOVA, Tomáš MARTÍNEK, Michaela VORLÍČKOVÁ, Boris VYSKOT and Eduard KEJNOVSKÝ. Guanine quadruplexes are formed by specific regions of human transposable elements. BMC Genomics. London: BioMed Central Ltd, 2014, vol. 15, No 1, p. 1032-1043. ISSN 1471-2164. Available from: https://dx.doi.org/10.1186/1471-2164-15-1032.
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Basic information
Original name Guanine quadruplexes are formed by specific regions of human transposable elements
Authors LEXA, Matej (703 Slovakia, guarantor, belonging to the institution), Pavlina STEFLOVA (203 Czech Republic), Tomáš MARTÍNEK (203 Czech Republic), Michaela VORLÍČKOVÁ (203 Czech Republic, belonging to the institution), Boris VYSKOT (203 Czech Republic) and Eduard KEJNOVSKÝ (203 Czech Republic).
Edition BMC Genomics, London, BioMed Central Ltd, 2014, 1471-2164.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10602 Biology , Evolutionary biology
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 3.986
RIV identification code RIV/00216224:14330/14:00077524
Organization unit Faculty of Informatics
Doi http://dx.doi.org/10.1186/1471-2164-15-1032
UT WoS 000355992300001
Keywords (in Czech) G4 kvadruplex; lidsky genom; transposony; cirkularni dichroismus; Bioconductor; bioinformatika
Keywords in English G4 quadruplex; human transposable elements; circular dichroism; Bioconductor code; bioinformatics
Tags International impact, Reviewed
Changed by Changed by: doc. Ing. Matej Lexa, Ph.D., učo 31298. Changed: 13/3/2018 14:08.
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.
Links
CZ.1.05/1.1.00/02.0068, interní kód MUName: CEITEC - středoevropský technologický institut (Acronym: CEITEC)
Investor: Ministry of Education, Youth and Sports of the CR, CEITEC - Central European Institute of Technology, 1.1 European Centres of Excellence
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