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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F22%3A00551529" target="_blank" >RIV/68081707:_____/22:00551529 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14310/22:00125544

Result on the web

<a href="https://www.sciencedirect.com/science/article/pii/S0378111921006533?via%3Dihub" target="_blank" >https://www.sciencedirect.com/science/article/pii/S0378111921006533?via%3Dihub</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.gene.2021.146058" target="_blank" >10.1016/j.gene.2021.146058</a>

Result language

angličtina

Original language name

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

Original language description

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.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10603 - Genetics and heredity (medical genetics to be 3)

Project

<a href="/en/project/GA18-15548S" target="_blank" >GA18-15548S: Comparative study of DNA interacting properties of the tumor suppressor p53 protein isoforms</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2022

Confidentiality

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

Name of the periodical

Gene

ISSN

0378-1119

e-ISSN

1879-0038

Volume of the periodical

810

Issue of the periodical within the volume

FEB 5 2022

Country of publishing house

NL - THE KINGDOM OF THE NETHERLANDS

Number of pages

5

Pages from-to

146058

UT code for WoS article

000735926800005

EID of the result in the Scopus database

2-s2.0-85118988535