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

J 2022

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

DOBROVOLNÁ, Michaela; Natália BOHÁLOVÁ; Vratislav PEŠKA; Jiawei WANG; Yu LUO et al.

Základní údaje

Originální název

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

Autoři

DOBROVOLNÁ, Michaela; Natália BOHÁLOVÁ; Vratislav PEŠKA; Jiawei WANG; Yu LUO; Martin BARTAS; Adriana VOLNÁ; Jean-Louis MERGNY a Václav BRÁZDA

Vydání

International Journal of Molecular Sciences, MDPI, 2022, 1422-0067

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Švýcarsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/22:00127696

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

G-quadruplex; G4 propensity; chloroplast DNA; sequence prediction

Štítky

14314010, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 4. 1. 2023 15:02, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

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.

Citovat

DOBROVOLNÁ, Michaela; Natália BOHÁLOVÁ; Vratislav PEŠKA; Jiawei WANG; Yu LUO; Martin BARTAS; Adriana VOLNÁ; Jean-Louis MERGNY a Václav BRÁZDA. The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation. International Journal of Molecular Sciences. MDPI, 2022, roč. 23, č. 15, s. 1-12. ISSN 1422-0067. Dostupné z: https://doi.org/10.3390/ijms23158482.

@article{2243555,
   author = {Dobrovolná, Michaela and Bohálová, Natália and Peška, Vratislav and Wang, Jiawei and Luo, Yu and Bartas, Martin and Volná, Adriana and Mergny, JeanandLouis and Brázda, Václav},
   article_number = {15},
   doi = {https://doi.org/10.3390/ijms23158482},
   keywords = {G-quadruplex; G4 propensity; chloroplast DNA; sequence prediction},
   language = {eng},
   issn = {1422-0067},
   journal = {International Journal of Molecular Sciences},
   title = {The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation},
   url = {https://www.mdpi.com/1422-0067/23/15/8482},
   volume = {23},
   year = {2022}
}

TY  - JOUR
ID  - 2243555
AU  - Dobrovolná, Michaela - Bohálová, Natália - Peška, Vratislav - Wang, Jiawei - Luo, Yu - Bartas, Martin - Volná, Adriana - Mergny, Jean-Louis - Brázda, Václav
PY  - 2022
TI  - The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation
JF  - International Journal of Molecular Sciences
VL  - 23
IS  - 15
SP  - 1-12
EP  - 1-12
PB  - MDPI
SN  - 14220067
KW  - G-quadruplex
KW  - G4 propensity
KW  - chloroplast DNA
KW  - sequence prediction
UR  - https://www.mdpi.com/1422-0067/23/15/8482
N2  - 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.
ER  -

DOBROVOLNÁ, Michaela; Natália BOHÁLOVÁ; Vratislav PEŠKA; Jiawei WANG; Yu LUO; Martin BARTAS; Adriana VOLNÁ; Jean-Louis MERGNY a Václav BRÁZDA. The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation. \textit{International Journal of Molecular Sciences}. MDPI, 2022, roč.~23, č.~15, s.~1-12. ISSN~1422-0067. Dostupné z: https://doi.org/10.3390/ijms23158482.

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