New telomere to telomere assembly of human chromosome 8 reveals
a previous underestimation of G-quadruplex forming sequences
and inverted repeats

J 2022

New telomere to telomere assembly of human chromosome 8 reveals a previous underestimation of G-quadruplex forming sequences and inverted repeats

BRÁZDA, Václav; Natália BOHÁLOVÁ a Richard P. BOWATER

Základní údaje

Originální název

New telomere to telomere assembly of human chromosome 8 reveals a previous underestimation of G-quadruplex forming sequences and inverted repeats

Autoři

BRÁZDA, Václav; Natália BOHÁLOVÁ a Richard P. BOWATER

Vydání

Gene, Amsterdam, Elsevier Science, 2022, 0378-1119

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10603 Genetics and heredity

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 3.500

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/22:00125544

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

G-quadruplex; Inverted repeat; Genome sequence of human chromosome 8; Non-B DNA structures

Štítky

14314010, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 21. 3. 2022 10:04, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

Taking advantage of evolving and improving sequencing methods, human chromosome 8 is now available as a gapless, end-to-end assembly. Thanks to advances in long-read sequencing technologies, its centromere, telomeres, duplicated gene families and repeat-rich regions are now fully sequenced. We were interested to assess if the new assembly altered our understanding of the potential impact of non-B DNA structures within this completed chromosome sequence. It has been shown that non-B secondary structures, such as G-quadruplexes, hairpins and cruciforms, have important regulatory functions and potential as targeted therapeutics. Therefore, we analysed the presence of putative G-quadruplex forming sequences and inverted repeats in the current human reference genome (GRCh38) and in the new end-to-end assembly of chromosome 8. The comparison revealed that the new assembly contains significantly more inverted repeats and G-quadruplex forming sequences compared to the current reference sequence. This observation can be explained by improved accuracy of the new sequencing methods, particularly in regions that contain extensive repeats of bases, as is preferred by many nonB DNA structures. These results show a significant underestimation of the prevalence of non-B DNA secondary structure in previous assembly versions of the human genome and point to their importance being not fully appreciated. We anticipate that similar observations will occur as the improved sequencing technologies fill in gaps across the genomes of humans and other organisms.

Citovat

BRÁZDA, Václav; Natália BOHÁLOVÁ a Richard P. BOWATER. New telomere to telomere assembly of human chromosome 8 reveals a previous underestimation of G-quadruplex forming sequences and inverted repeats. Gene. Amsterdam: Elsevier Science, 2022, roč. 810, February, s. 146058-146062. ISSN 0378-1119. Dostupné z: https://doi.org/10.1016/j.gene.2021.146058.

@article{1842098,
   author = {Brázda, Václav and Bohálová, Natália and Bowater, Richard P.},
   article_location = {Amsterdam},
   article_number = {February},
   doi = {https://doi.org/10.1016/j.gene.2021.146058},
   keywords = {G-quadruplex; Inverted repeat; Genome sequence of human chromosome 8; Non-B DNA structures},
   language = {eng},
   issn = {0378-1119},
   journal = {Gene},
   title = {New telomere to telomere assembly of human chromosome 8 reveals a previous underestimation of G-quadruplex forming sequences and inverted repeats},
   url = {https://www.sciencedirect.com/science/article/pii/S0378111921006533},
   volume = {810},
   year = {2022}
}

TY  - JOUR
ID  - 1842098
AU  - Brázda, Václav - Bohálová, Natália - Bowater, Richard P.
PY  - 2022
TI  - New telomere to telomere assembly of human chromosome 8 reveals a previous underestimation of G-quadruplex forming sequences and inverted repeats
JF  - Gene
VL  - 810
IS  - February
SP  - 146058
EP  - 146058
PB  - Elsevier Science
SN  - 03781119
KW  - G-quadruplex
KW  - Inverted repeat
KW  - Genome sequence of human chromosome 8
KW  - Non-B DNA structures
UR  - https://www.sciencedirect.com/science/article/pii/S0378111921006533
N2  - Taking advantage of evolving and improving sequencing methods, human chromosome 8 is now available as a gapless, end-to-end assembly. Thanks to advances in long-read sequencing technologies, its centromere, telomeres, duplicated gene families and repeat-rich regions are now fully sequenced. We were interested to assess if the new assembly altered our understanding of the potential impact of non-B DNA structures within this completed chromosome sequence. It has been shown that non-B secondary structures, such as G-quadruplexes, hairpins and cruciforms, have important regulatory functions and potential as targeted therapeutics. Therefore, we analysed the presence of putative G-quadruplex forming sequences and inverted repeats in the current human reference genome (GRCh38) and in the new end-to-end assembly of chromosome 8. The comparison revealed that the new assembly contains significantly more inverted repeats and G-quadruplex forming sequences compared to the current reference sequence. This observation can be explained by improved accuracy of the new sequencing methods, particularly in regions that contain extensive repeats of bases, as is preferred by many nonB DNA structures. These results show a significant underestimation of the prevalence of non-B DNA secondary structure in previous assembly versions of the human genome and point to their importance being not fully appreciated. We anticipate that similar observations will occur as the improved sequencing technologies fill in gaps across the genomes of humans and other organisms.
ER  -

BRÁZDA, Václav; Natália BOHÁLOVÁ a Richard P. BOWATER. New telomere to telomere assembly of human chromosome 8 reveals a previous underestimation of G-quadruplex forming sequences and inverted repeats. \textit{Gene}. Amsterdam: Elsevier Science, 2022, roč.~810, February, s.~146058-146062. ISSN~0378-1119. Dostupné z: https://doi.org/10.1016/j.gene.2021.146058.

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