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Novel G-quadruplex prone sequences emerge in the complete assembly of the human X chromosome
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SYSNO ASEP 0546407 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Novel G-quadruplex prone sequences emerge in the complete assembly of the human X chromosome Author(s) Bohalova, Natalia (BFU-R) ORCID
Mergny, Jean-Louis (BFU-R) ORCID, RID
Brázda, Václav (BFU-R) RID, ORCIDNumber of authors 3 Source Title Biochimie. - : Elsevier - ISSN 0300-9084
Roč. 191, DEC 2021 (2021), s. 87-90Number of pages 4 s. Publication form Print - P Language eng - English Country FR - France Keywords G-quadruplex ; Chromosome X ; G4Hunter ; Bioinformatics ; Non-B DNA Subject RIV CE - Biochemistry OECD category Biochemistry and molecular biology R&D Projects EF15_003/0000477 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Method of publishing Limited access Institutional support BFU-R - RVO:68081707 UT WOS 000701719900010 EID SCOPUS 85114663707 DOI 10.1016/j.biochi.2021.09.004 Annotation 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/). Workplace Institute of Biophysics Contact Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244 Year of Publishing 2022 Electronic address https://www.sciencedirect.com/science/article/pii/S0300908421002078?via%3Dihub
Number of the records: 1