Novel G-quadruplex prone sequences emerge in the complete
assembly of the human X chromosome

J 2021

Novel G-quadruplex prone sequences emerge in the complete assembly of the human X chromosome

BOHÁLOVÁ, Natália; Jean-Louis MERGNY a Václav BRÁZDA

Základní údaje

Originální název

Novel G-quadruplex prone sequences emerge in the complete assembly of the human X chromosome

Autoři

BOHÁLOVÁ, Natália; Jean-Louis MERGNY a Václav BRÁZDA

Vydání

Biochimie, Elsevier, 2021, 0300-9084

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Francie

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.372

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/21:00123515

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

G-quadruplex; Chromosome X; G4Hunter; Bioinformatics; Non-B DNA

Štítky

14314010, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 6. 1. 2022 12:03, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

G-quadruplexes are non-B secondary structures with regulatory functions and therapeutic potential. Improvements in sequencing methods recently allowed the completion of the first human chromosome which is now available as a gapless, end-to-end assembly, with the previously remaining spaces filled and newly identified regions added. We compared the presence of G-quadruplex forming sequences in the current human reference genome (GRCh38) and in the new end-to-end assembly of the X chromosome constructed by high-coverage ultra-long-read nanopore sequencing. This comparison revealed that, even though the corrected length of the chromosome X assembly is surprisingly 1.14% shorter than expected, the number of G-quadruplex forming sequences found in this gapless chromosome is significantly higher, with 493 new motifs having G4Hunter scores above 1.4 and 23 new sequences with G4Hunter scores above 3.5. This observation reflects an improved precision of the new sequencing approaches and points to an underestimation of G-quadruplex propensity in the previous, widely used version of the human genome assembly, especially for motifs with a high G4Hunter score, expected to be very stable. These G-quadruplex forming sequences probably remained undiscovered in earlier genome datasets due to previously unsolved G-rich and repetitive genomic regions. These observations allow a precise targeting of these important regulatory regions.

Citovat

BOHÁLOVÁ, Natália; Jean-Louis MERGNY a Václav BRÁZDA. Novel G-quadruplex prone sequences emerge in the complete assembly of the human X chromosome. Biochimie. Elsevier, 2021, roč. 191, December, s. 87-90. ISSN 0300-9084. Dostupné z: https://doi.org/10.1016/j.biochi.2021.09.004.

@article{1817058,
   author = {Bohálová, Natália and Mergny, JeanandLouis and Brázda, Václav},
   article_number = {December},
   doi = {https://doi.org/10.1016/j.biochi.2021.09.004},
   keywords = {G-quadruplex; Chromosome X; G4Hunter; Bioinformatics; Non-B DNA},
   language = {eng},
   issn = {0300-9084},
   journal = {Biochimie},
   title = {Novel G-quadruplex prone sequences emerge in the complete assembly of the human X chromosome},
   url = {https://www.sciencedirect.com/science/article/pii/S0300908421002078#!},
   volume = {191},
   year = {2021}
}

TY  - JOUR
ID  - 1817058
AU  - Bohálová, Natália - Mergny, Jean-Louis - Brázda, Václav
PY  - 2021
TI  - Novel G-quadruplex prone sequences emerge in the complete assembly of the human X chromosome
JF  - Biochimie
VL  - 191
IS  - December
SP  - 87-90
EP  - 87-90
PB  - Elsevier
SN  - 03009084
KW  - G-quadruplex
KW  - Chromosome X
KW  - G4Hunter
KW  - Bioinformatics
KW  - Non-B DNA
UR  - https://www.sciencedirect.com/science/article/pii/S0300908421002078#!
N2  - G-quadruplexes are non-B secondary structures with regulatory functions and therapeutic potential. Improvements in sequencing methods recently allowed the completion of the first human chromosome which is now available as a gapless, end-to-end assembly, with the previously remaining spaces filled and newly identified regions added. We compared the presence of G-quadruplex forming sequences in the current human reference genome (GRCh38) and in the new end-to-end assembly of the X chromosome constructed by high-coverage ultra-long-read nanopore sequencing. This comparison revealed that, even though the corrected length of the chromosome X assembly is surprisingly 1.14% shorter than expected, the number of G-quadruplex forming sequences found in this gapless chromosome is significantly higher, with 493 new motifs having G4Hunter scores above 1.4 and 23 new sequences with G4Hunter scores above 3.5. This observation reflects an improved precision of the new sequencing approaches and points to an underestimation of G-quadruplex propensity in the previous, widely used version of the human genome assembly, especially for motifs with a high G4Hunter score, expected to be very stable. These G-quadruplex forming sequences probably remained undiscovered in earlier genome datasets due to previously unsolved G-rich and repetitive genomic regions. These observations allow a precise targeting of these important regulatory regions.
ER  -

BOHÁLOVÁ, Natália; Jean-Louis MERGNY a Václav BRÁZDA. Novel G-quadruplex prone sequences emerge in the complete assembly of the human X chromosome. \textit{Biochimie}. Elsevier, 2021, roč.~191, December, s.~87-90. ISSN~0300-9084. Dostupné z: https://doi.org/10.1016/j.biochi.2021.09.004.

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