The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation

Dobrovolná, Michaela; Bohalova, Natalia; Peška, Vratislav; Wang, J.; Luo, Y.; Bartas, M.; Volna, A.; Mergny, Jean-Louis; Brázda, Václav

doi:https://dx.doi.org/10.3390/ijms23158482

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The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation

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SYSNO ASEP	0560261
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation
Author(s)	Dobrovolná, Michaela (BFU-R) Bohalova, Natalia (BFU-R)_ORCID Peška, Vratislav (BFU-R)_{RID, ORCID} Wang, J. (FR) Luo, Y. (FR) Bartas, M. (CZ) Volna, A. (CZ) Mergny, Jean-Louis (BFU-R)_{ORCID, RID} Brázda, Václav (BFU-R)_{RID, ORCID}
Number of authors	9
Article number	8482
Source Title	International Journal of Molecular Sciences. - : MDPI Roč. 23, č. 15 (2022)
Number of pages	12 s.
Publication form	Online - E
Language	eng - English
Country	CH - Switzerland
Keywords	G-quadruplex ; G4 propensity ; chloroplast DNA ; sequence prediction
Subject RIV	CE - Biochemistry
OECD category	Biochemistry and molecular biology
R&D Projects	EF15_003/0000477 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
	GA22-21903S GA ČR - Czech Science Foundation (CSF)
Method of publishing	Open access
Institutional support	BFU-R - RVO:68081707
UT WOS	000838851900001
EID SCOPUS	85137096504
DOI	10.3390/ijms23158482
Annotation	G-quadruplexes (G4s) have been long considered rare and physiologically unimportant in vitro curiosities, but recent methodological advances have proved their presence and functions in vivo. Moreover, in addition to their functional relevance in bacteria and animals, including humans, their importance has been recently demonstrated in evolutionarily distinct plant species. In this study, we analyzed the genome of Pisum sativum (garden pea, or the so-called green pea), a unique member of the Fabaceae family. Our results showed that this genome contained putative G4 sequences (PQSs). Interestingly, these PQSs were located nonrandomly in the nuclear genome. We also found PQSs in mitochondrial (mt) and chloroplast (cp) DNA, and we experimentally confirmed G4 formation for sequences found in these two organelles. The frequency of PQSs for nuclear DNA was 0.42 PQSs per thousand base pairs (kbp), in the same range as for cpDNA (0.53/kbp), but significantly lower than what was found for mitochondrial DNA (1.58/kbp). In the nuclear genome, PQSs were mainly associated with regulatory regions, including 5 ' UTRs, and upstream of the rRNA region. In contrast to genomic DNA, PQSs were located around RNA genes in cpDNA and mtDNA. Interestingly, PQSs were also associated with specific transposable elements such as TIR and LTR and around them, pointing to their role in their spreading in nuclear DNA. The nonrandom localization of PQSs uncovered their evolutionary and functional significance in the Pisum sativum genome.
Workplace	Institute of Biophysics
Contact	Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244
Year of Publishing	2023
Electronic address	https://www.mdpi.com/1422-0067/23/15/8482

Number of the records: 1