Guanine quadruplexes are formed by specific regions of human
transposable elements

J 2014

Guanine quadruplexes are formed by specific regions of human transposable elements

LEXA, Matej, Pavlina STEFLOVA, Tomáš MARTÍNEK, Michaela VORLÍČKOVÁ, Boris VYSKOT et. al.

Základní údaje

Originální název

Guanine quadruplexes are formed by specific regions of human transposable elements

Autoři

LEXA, Matej (703 Slovensko, garant, domácí), Pavlina STEFLOVA (203 Česká republika), Tomáš MARTÍNEK (203 Česká republika), Michaela VORLÍČKOVÁ (203 Česká republika, domácí), Boris VYSKOT (203 Česká republika) a Eduard KEJNOVSKÝ (203 Česká republika)

Vydání

BMC Genomics, London, BioMed Central Ltd, 2014, 1471-2164

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10602 Biology , Evolutionary biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.986

Kód RIV

RIV/00216224:14330/14:00077524

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1186/1471-2164-15-1032

UT WoS

000355992300001

Klíčová slova česky

G4 kvadruplex; lidsky genom; transposony; cirkularni dichroismus; Bioconductor; bioinformatika

Klíčová slova anglicky

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

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 13. 3. 2018 14:08, doc. Ing. Matej Lexa, Ph.D.

Anotace

V originále

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.

Návaznosti

CZ.1.05/1.1.00/02.0068, interní kód MU

Název: CEITEC - středoevropský technologický institut (Akronym: CEITEC)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC - středoevropský technologický institut, 1.1 Evropská centra excelence

Citovat

LEXA, Matej, Pavlina STEFLOVA, Tomáš MARTÍNEK, Michaela VORLÍČKOVÁ, Boris VYSKOT a Eduard KEJNOVSKÝ. Guanine quadruplexes are formed by specific regions of human transposable elements. BMC Genomics. London: BioMed Central Ltd, 2014, roč. 15, č. 1, s. 1032-1043. ISSN 1471-2164. Dostupné z: https://dx.doi.org/10.1186/1471-2164-15-1032.

@article{1210725,
   author = {Lexa, Matej and Steflova, Pavlina and Martínek, Tomáš and Vorlíčková, Michaela and Vyskot, Boris and Kejnovský, Eduard},
   article_location = {London},
   article_number = {1},
   doi = {http://dx.doi.org/10.1186/1471-2164-15-1032},
   keywords = {G4 quadruplex; human transposable elements; circular dichroism; Bioconductor code; bioinformatics},
   language = {eng},
   issn = {1471-2164},
   journal = {BMC Genomics},
   title = {Guanine quadruplexes are formed by specific regions of human transposable elements},
   url = {http://www.biomedcentral.com/1471-2164/15/1032},
   volume = {15},
   year = {2014}
}

TY  - JOUR
ID  - 1210725
AU  - Lexa, Matej - Steflova, Pavlina - Martínek, Tomáš - Vorlíčková, Michaela - Vyskot, Boris - Kejnovský, Eduard
PY  - 2014
TI  - Guanine quadruplexes are formed by specific regions of human transposable elements
JF  - BMC Genomics
VL  - 15
IS  - 1
SP  - 1032
EP  - 1032
PB  - BioMed Central Ltd
SN  - 14712164
KW  - G4 quadruplex
KW  - human transposable elements
KW  - circular dichroism
KW  - Bioconductor code
KW  - bioinformatics
UR  - http://www.biomedcentral.com/1471-2164/15/1032
N2  - 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.
ER  -

LEXA, Matej, Pavlina STEFLOVA, Tomáš MARTÍNEK, Michaela VORLÍČKOVÁ, Boris VYSKOT a Eduard KEJNOVSKÝ. Guanine quadruplexes are formed by specific regions of human transposable elements. \textit{BMC Genomics}. London: BioMed Central Ltd, 2014, roč.~15, č.~1, s.~1032-1043. ISSN~1471-2164. Dostupné z: https://dx.doi.org/10.1186/1471-2164-15-1032.

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