Publication result detail

Complete analysis of G-quadruplex forming sequences in the gapless assembly of human chromosome Y

DOBROVOLNÁ, M.; MERGNY, J-L.; BRÁZDA, V.

Original Title

Complete analysis of G-quadruplex forming sequences in the gapless assembly of human chromosome Y

English Title

Complete analysis of G-quadruplex forming sequences in the gapless assembly of human chromosome Y

Type

WoS Article

Original Abstract

Recent advancements have finally delivered a complete human genome assembly, including the elusive Y chromosome. This accomplishment closes a significant knowledge gap. Prior efforts were hampered by challenges in sequencing repetitive DNA structures such as direct and inverted repeats. We used the G4Hunter algorithm to analyze the presence of G-quadruplex forming sequences (G4s) within the current human reference genome (GRCh38) and the new telomere-to-telomere (T2T) Y chromosome assemblies. This analysis served a dual purpose: identifying the location of potential G4s within the genomes and exploring their association with functionally annotated sequences. Compared to GRCh38, the T2T assembly exhibited a significantly higher prevalence of G-quadruplex forming sequences. Notably, these repeats were abundantly located around precursor RNA, exons, genes, and within protein binding sites. This remarkable co-occurrence of G4-forming sequences with these critical regulatory regions suggests their role in fundamental DNA regulation processes. Our findings indicate that the current human reference genome significantly underestimated the number of G4s, potentially overlooking their functional importance. (c) 2024 Elsevier B.V. and Soci & eacute;t & eacute; Fran & ccedil;aise de Biochimie et Biologie Mol & eacute;culaire (SFBBM). All rights are reserved, including those for text and data mining, AI training, and similar technologies.

English abstract

Recent advancements have finally delivered a complete human genome assembly, including the elusive Y chromosome. This accomplishment closes a significant knowledge gap. Prior efforts were hampered by challenges in sequencing repetitive DNA structures such as direct and inverted repeats. We used the G4Hunter algorithm to analyze the presence of G-quadruplex forming sequences (G4s) within the current human reference genome (GRCh38) and the new telomere-to-telomere (T2T) Y chromosome assemblies. This analysis served a dual purpose: identifying the location of potential G4s within the genomes and exploring their association with functionally annotated sequences. Compared to GRCh38, the T2T assembly exhibited a significantly higher prevalence of G-quadruplex forming sequences. Notably, these repeats were abundantly located around precursor RNA, exons, genes, and within protein binding sites. This remarkable co-occurrence of G4-forming sequences with these critical regulatory regions suggests their role in fundamental DNA regulation processes. Our findings indicate that the current human reference genome significantly underestimated the number of G4s, potentially overlooking their functional importance. (c) 2024 Elsevier B.V. and Soci & eacute;t & eacute; Fran & ccedil;aise de Biochimie et Biologie Mol & eacute;culaire (SFBBM). All rights are reserved, including those for text and data mining, AI training, and similar technologies.

Keywords

Gapless assembly; Chromosome Y; G-quadruplex; Genome analysis

Key words in English

Gapless assembly; Chromosome Y; G-quadruplex; Genome analysis

Authors

DOBROVOLNÁ, M.; MERGNY, J-L.; BRÁZDA, V.

RIV year

2025

Released

09.10.2024

Publisher

ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER

Location

ISSY-LES-MOULINEAUX

ISBN

1638-6183

Periodical

BIOCHIMIE

Volume

229

Number

February

State

French Republic

Pages from

49

Pages to

57

Pages count

9

URL

https://pubmed.ncbi.nlm.nih.gov/39389449/

BibTex

@article{BUT190101,
  author="DOBROVOLNÁ, M. and MERGNY, J-L. and BRÁZDA, V.",
  title="Complete analysis of G-quadruplex forming sequences in the gapless assembly of human chromosome Y",
  journal="BIOCHIMIE",
  year="2024",
  volume="229",
  number="February",
  pages="49--57",
  doi="10.1016/j.biochi.2024.10.007",
  issn="0300-9084",
  url="https://pubmed.ncbi.nlm.nih.gov/39389449/"
}