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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F21%3A00546407" target="_blank" >RIV/68081707:_____/21:00546407 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14310/21:00123515

Result on the web

<a href="https://www.sciencedirect.com/science/article/pii/S0300908421002078?via%3Dihub" target="_blank" >https://www.sciencedirect.com/science/article/pii/S0300908421002078?via%3Dihub</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.biochi.2021.09.004" target="_blank" >10.1016/j.biochi.2021.09.004</a>

Result language

angličtina

Original language name

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

Original language description

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. (c) 2021 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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

10608 - Biochemistry and molecular biology

Project

<a href="/en/project/EF15_003%2F0000477" target="_blank" >EF15_003/0000477: Structural gymnastics of nucleic acids: from molecular principles through biological functions to therapeutic targets.</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2021

Confidentiality

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

Name of the periodical

Biochimie

ISSN

0300-9084

e-ISSN

1638-6183

Volume of the periodical

191

Issue of the periodical within the volume

DEC 2021

Country of publishing house

FR - FRANCE

Number of pages

4

Pages from-to

87-90

UT code for WoS article

000701719900010

EID of the result in the Scopus database

2-s2.0-85114663707