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TOKAN, Viktor, Janka PUTEROVÁ, Matej LEXA and Eduard KEJNOVSKÝ. Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast. BMC Genomics. BioMed Central, 2018, vol. 19, 06 03 2018, p. 184-194. ISSN 1471-2164. Available from: https://dx.doi.org/10.1186/s12864-018-4563-7.

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TY  - JOUR
ID  - 1410241
AU  - Tokan, Viktor - Puterová, Janka - Lexa, Matej - Kejnovský, Eduard
PY  - 2018
TI  - Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast
JF  - BMC Genomics
VL  - 19
IS  - 06 03 2018
SP  - 184
EP  - 184
PB  - BioMed Central
SN  - 14712164
KW  - G4 motifs
KW  - Quadruplex DNA
KW  - Transposable elements
KW  - Maize LTR retrotransposons
KW  - Circular dichroism
KW  - NMM ligand
UR  - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4563-7
L2  - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4563-7
N2  - Background Many studies have shown that guanine-rich DNA sequences form quadruplex structures (G4) in vitro but there is scarce evidence of guanine quadruplexes in vivo. The majority of potential quadruplex-forming sequences (PQS) are located in transposable elements (TEs), especially close to promoters within long terminal repeats of plant LTR retrotransposons. Results In order to test the potential effect of G4s on retrotransposon expression, we cloned the long terminal repeats of selected maize LTR retrotransposons upstream of the lacZ reporter gene and measured its transcription and translation in yeast. We found that G4s had an inhibitory effect on translation in vivo since “mutants” (where guanines were replaced by adenines in PQS) showed higher expression levels than wild-types. In parallel, we confirmed by circular dichroism measurements that the selected sequences can indeed adopt G4 conformation in vitro. Analysis of RNA-Seq of polyA RNA in maize seedlings grown in the presence of a G4-stabilizing ligand (NMM) showed both inhibitory as well as stimulatory effects on the transcription of LTR retrotransposons. Conclusions Our results demonstrate that quadruplex DNA located within long terminal repeats of LTR retrotransposons can be formed in vivo and that it plays a regulatory role in the LTR retrotransposon life-cycle, thus also affecting genome dynamics.
ER  -

Basic information
Original name	Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast
Authors	TOKAN, Viktor (203 Czech Republic, guarantor), Janka PUTEROVÁ (703 Slovakia), Matej LEXA (703 Slovakia, belonging to the institution) and Eduard KEJNOVSKÝ (203 Czech Republic).
Edition	BMC Genomics, BioMed Central, 2018, 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: 3.501
RIV identification code	RIV/00216224:14330/18:00100852
Organization unit	Faculty of Informatics
Doi	http://dx.doi.org/10.1186/s12864-018-4563-7
UT WoS	000427128900005
Keywords in English	G4 motifs; Quadruplex DNA; Transposable elements; Maize LTR retrotransposons; Circular dichroism; NMM ligand
Tags	International impact, Reviewed
Changed by	Changed by: doc. Ing. Matej Lexa, Ph.D., učo 31298. Changed: 2/10/2018 15:06.

Abstract
Background Many studies have shown that guanine-rich DNA sequences form quadruplex structures (G4) in vitro but there is scarce evidence of guanine quadruplexes in vivo. The majority of potential quadruplex-forming sequences (PQS) are located in transposable elements (TEs), especially close to promoters within long terminal repeats of plant LTR retrotransposons. Results In order to test the potential effect of G4s on retrotransposon expression, we cloned the long terminal repeats of selected maize LTR retrotransposons upstream of the lacZ reporter gene and measured its transcription and translation in yeast. We found that G4s had an inhibitory effect on translation in vivo since “mutants” (where guanines were replaced by adenines in PQS) showed higher expression levels than wild-types. In parallel, we confirmed by circular dichroism measurements that the selected sequences can indeed adopt G4 conformation in vitro. Analysis of RNA-Seq of polyA RNA in maize seedlings grown in the presence of a G4-stabilizing ligand (NMM) showed both inhibitory as well as stimulatory effects on the transcription of LTR retrotransposons. Conclusions Our results demonstrate that quadruplex DNA located within long terminal repeats of LTR retrotransposons can be formed in vivo and that it plays a regulatory role in the LTR retrotransposon life-cycle, thus also affecting genome dynamics.

Abstract

Background Many studies have shown that guanine-rich DNA sequences form quadruplex structures (G4) in vitro but there is scarce evidence of guanine quadruplexes in vivo. The majority of potential quadruplex-forming sequences (PQS) are located in transposable elements (TEs), especially close to promoters within long terminal repeats of plant LTR retrotransposons. Results In order to test the potential effect of G4s on retrotransposon expression, we cloned the long terminal repeats of selected maize LTR retrotransposons upstream of the lacZ reporter gene and measured its transcription and translation in yeast. We found that G4s had an inhibitory effect on translation in vivo since “mutants” (where guanines were replaced by adenines in PQS) showed higher expression levels than wild-types. In parallel, we confirmed by circular dichroism measurements that the selected sequences can indeed adopt G4 conformation in vitro. Analysis of RNA-Seq of polyA RNA in maize seedlings grown in the presence of a G4-stabilizing ligand (NMM) showed both inhibitory as well as stimulatory effects on the transcription of LTR retrotransposons. Conclusions Our results demonstrate that quadruplex DNA located within long terminal repeats of LTR retrotransposons can be formed in vivo and that it plays a regulatory role in the LTR retrotransposon life-cycle, thus also affecting genome dynamics.

Links
GA15-02891S, research and development project	Name: Rostlinné transpozony a konformace DNA
GA15-02891S, research and development project	Investor: Czech Science Foundation