Quadruplex-forming sequences occupy discrete regions inside
plant LTR retrotransposons

J 2014

Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons

LEXA, Matej, Eduard KEJNOVSKÝ, Pavlína ŠTEFLOVÁ, Helena KONVALINOVÁ, Michaela VORLÍČKOVÁ et. al.

Základní údaje

Originální název

Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons

Autoři

LEXA, Matej (703 Slovensko, garant, domácí), Eduard KEJNOVSKÝ (203 Česká republika), Pavlína ŠTEFLOVÁ (203 Česká republika, domácí), Helena KONVALINOVÁ (203 Česká republika, domácí), Michaela VORLÍČKOVÁ (203 Česká republika, domácí) a Boris VYSKOT (203 Česká republika)

Vydání

Nucleic Acids Research, Oxford, Oxford University Press, 2014, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 9.112

Kód RIV

RIV/00216224:14740/14:00074769

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1093/nar/gkt893

UT WoS

000331138100030

Klíčová slova anglicky

INTRAMOLECULAR DNA QUADRUPLEXES; VIRUS TYPE-1 RNA; CIRCULAR-DICHROISM; GUANINE QUADRUPLEXES; HUMAN GENOME; IN-VIVO; IDENTIFICATION; STABILITY; BINDING; TRIPLEX

Štítky

kontrola MP, OA, ok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 13. 3. 2018 14:15, doc. Ing. Matej Lexa, Ph.D.

Anotace

V originále

Retrotransposons with long terminal repeats (LTR) form a significant proportion of eukaryotic genomes, especially in plants. They have gag and pol genes and several regulatory regions necessary for transcription and reverse transcription. We searched for potential quadruplex-forming sequences (PQSs) and potential triplex forming sequences (PTSs) in 18 377 full-length LTR retrotransposons collected from 21 plant species. We found that PQSs were often located in LTRs, both upstream and downstream of promoters from which the whole retrotransposon is transcribed. Upstream-located guanine PQSs were dominant in the minus DNA strand, whereas downstream-located guanine PQSs prevailed in the plus strand, indicating their role both at transcriptional and post-transcriptional levels. Our circular dichroism spectroscopy measurements confirmed that these PQSs readily adopted guanine quadruplex structures - some of them were paralell-stranded, while others were anti-parallel-stranded. The PQS often formed doublets at a mutual distance of up to 400 bp. PTSs were most abundant in 3'UTR (but were also present in 5'UTR). We discuss the potential role of quadruplexes and triplexes as the regulators of various processes participating in LTR retrotransposon life cycle and as potential recombination sites during post-insertional retrotransposon-based genome rearrangements.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

EE2.3.20.0045, projekt VaV

Název: Podpora profesního růstu a mezinárodní integrace výzkumných týmů v oblasti molekulární medicíny

Přiložené soubory

Vorlickova_NAR_2014-Lexa-968-78.pdf

Požádat o autorskou verzi souboru

Citovat

LEXA, Matej, Eduard KEJNOVSKÝ, Pavlína ŠTEFLOVÁ, Helena KONVALINOVÁ, Michaela VORLÍČKOVÁ a Boris VYSKOT. Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons. Nucleic Acids Research. Oxford: Oxford University Press, 2014, roč. 42, č. 2, s. 968-978. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkt893.

@article{1125230,
   author = {Lexa, Matej and Kejnovský, Eduard and Šteflová, Pavlína and Konvalinová, Helena and Vorlíčková, Michaela and Vyskot, Boris},
   article_location = {Oxford},
   article_number = {2},
   doi = {http://dx.doi.org/10.1093/nar/gkt893},
   keywords = {INTRAMOLECULAR DNA QUADRUPLEXES; VIRUS TYPE-1 RNA; CIRCULAR-DICHROISM; GUANINE QUADRUPLEXES; HUMAN GENOME; IN-VIVO; IDENTIFICATION; STABILITY; BINDING; TRIPLEX},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons},
   url = {http://nar.oxfordjournals.org/content/early/2013/10/07/nar.gkt893},
   volume = {42},
   year = {2014}
}

TY  - JOUR
ID  - 1125230
AU  - Lexa, Matej - Kejnovský, Eduard - Šteflová, Pavlína - Konvalinová, Helena - Vorlíčková, Michaela - Vyskot, Boris
PY  - 2014
TI  - Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons
JF  - Nucleic Acids Research
VL  - 42
IS  - 2
SP  - 968-978
EP  - 968-978
PB  - Oxford University Press
SN  - 03051048
KW  - INTRAMOLECULAR DNA QUADRUPLEXES
KW  - VIRUS TYPE-1 RNA
KW  - CIRCULAR-DICHROISM
KW  - GUANINE QUADRUPLEXES
KW  - HUMAN GENOME
KW  - IN-VIVO
KW  - IDENTIFICATION
KW  - STABILITY
KW  - BINDING
KW  - TRIPLEX
UR  - http://nar.oxfordjournals.org/content/early/2013/10/07/nar.gkt893
L2  - http://nar.oxfordjournals.org/content/early/2013/10/07/nar.gkt893
N2  - Retrotransposons with long terminal repeats (LTR) form a significant proportion of eukaryotic genomes, especially in plants. They have gag and pol genes and several regulatory regions necessary for transcription and reverse transcription. We searched for potential quadruplex-forming sequences (PQSs) and potential triplex forming sequences (PTSs) in 18 377 full-length LTR retrotransposons collected from 21 plant species. We found that PQSs were often located in LTRs, both upstream and downstream of promoters from which the whole retrotransposon is transcribed. Upstream-located guanine PQSs were dominant in the minus DNA strand, whereas downstream-located guanine PQSs prevailed in the plus strand, indicating their role both at transcriptional and post-transcriptional levels. Our circular dichroism spectroscopy measurements confirmed that these PQSs readily adopted guanine quadruplex structures - some of them were paralell-stranded, while others were anti-parallel-stranded. The PQS often formed doublets at a mutual distance of up to 400 bp. PTSs were most abundant in 3'UTR (but were also present in 5'UTR). We discuss the potential role of quadruplexes and triplexes as the regulators of various processes participating in LTR retrotransposon life cycle and as potential recombination sites during post-insertional retrotransposon-based genome rearrangements.
ER  -

LEXA, Matej, Eduard KEJNOVSKÝ, Pavlína ŠTEFLOVÁ, Helena KONVALINOVÁ, Michaela VORLÍČKOVÁ a Boris VYSKOT. Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2014, roč.~42, č.~2, s.~968-978. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkt893.

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