High-Resolution Assembly of the Human Y Chromosome Identifies a Vast Landscape of Inverted Repeats Associated with Structural and Functional Genomic Features

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F25%3A00640808" target="_blank" >RIV/68081707:_____/25:00640808 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/61988987:17310/25:A2603CYO RIV/00216305:26310/26:0200523

Výsledek na webu

<a href="https://www.mdpi.com/1422-0067/26/20/10180" target="_blank" >https://www.mdpi.com/1422-0067/26/20/10180</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3390/ijms262010180" target="_blank" >10.3390/ijms262010180</a>

Jazyk výsledku

angličtina

Název v původním jazyce

High-Resolution Assembly of the Human Y Chromosome Identifies a Vast Landscape of Inverted Repeats Associated with Structural and Functional Genomic Features

Popis výsledku v původním jazyce

Recent advances in sequencing methods have led to major progress in the gapless assemblies of the human genome. However, until mid-2023, the complete sequence of the Y chromosome remained elusive. While only a small percentage of autosomal chromosomes were without complete sequences in the broadly used reference assembly of the human genome (GRCh38), around 50% of the chromosome Y DNA sequence was unknown. Using a sophisticated computational approach, we analyzed the presence of short inverted repeats in the current human reference genome (GRCh38) and in the Telomere-to-Telomere (T2T) assembly of chromosome Y. This analysis identified the location of the repeats in chromosome Y and highlighted their association with functionally annotated sequences. The comparison revealed notably more inverted repeats in the T2T assembly compared to GRCh38. These are located abundantly around exons and mobile elements, and, unexpectedly, also within gene annotations. The remarkable abundance of short inverted repeats around exons points to their importance in gene regulation, and their presence in regions associated with recombination suggests crucial roles in recombination processes. Interestingly, the most underestimated sequences in the T2T assembly are inverted repeats with a repeat length of 12-14, which are more than 20 times as frequent as those in the human reference genome GRCh38. These findings indicate that the number of short inverted repeats was significantly underestimated in the current human reference genome (GRCh38). These previously unidentified sites are of great bio-medicinal potential, as inverted repeats are precursors for the formation of cruciform DNA functional epitopes.

Název v anglickém jazyce

High-Resolution Assembly of the Human Y Chromosome Identifies a Vast Landscape of Inverted Repeats Associated with Structural and Functional Genomic Features

Popis výsledku anglicky

Recent advances in sequencing methods have led to major progress in the gapless assemblies of the human genome. However, until mid-2023, the complete sequence of the Y chromosome remained elusive. While only a small percentage of autosomal chromosomes were without complete sequences in the broadly used reference assembly of the human genome (GRCh38), around 50% of the chromosome Y DNA sequence was unknown. Using a sophisticated computational approach, we analyzed the presence of short inverted repeats in the current human reference genome (GRCh38) and in the Telomere-to-Telomere (T2T) assembly of chromosome Y. This analysis identified the location of the repeats in chromosome Y and highlighted their association with functionally annotated sequences. The comparison revealed notably more inverted repeats in the T2T assembly compared to GRCh38. These are located abundantly around exons and mobile elements, and, unexpectedly, also within gene annotations. The remarkable abundance of short inverted repeats around exons points to their importance in gene regulation, and their presence in regions associated with recombination suggests crucial roles in recombination processes. Interestingly, the most underestimated sequences in the T2T assembly are inverted repeats with a repeat length of 12-14, which are more than 20 times as frequent as those in the human reference genome GRCh38. These findings indicate that the number of short inverted repeats was significantly underestimated in the current human reference genome (GRCh38). These previously unidentified sites are of great bio-medicinal potential, as inverted repeats are precursors for the formation of cruciform DNA functional epitopes.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

<a href="/cs/project/GA22-21903S" target="_blank" >GA22-21903S: Lokální struktury DNA a jejich role ve funkci mutantního proteinu p53 z lidských nádorů</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2025

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

International Journal of Molecular Sciences

ISSN

1661-6596

e-ISSN

1422-0067

Svazek periodika

26

Číslo periodika v rámci svazku

20

Stát vydavatele periodika

CH - Švýcarská konfederace

Počet stran výsledku

16

Strana od-do

10180

Kód UT WoS článku

001601716600001

EID výsledku v databázi Scopus

2-s2.0-105020065741