SARS-CoV-2 hot-spot mutations are significantly enriched within
inverted repeats and CpG island loci

J 2021

SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci

GOSWAMI, Pratik, Martin BARTAS, Matej LEXA, Natália BOHÁLOVÁ, Adriana VOLNÁ et. al.

Základní údaje

Originální název

SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci

Autoři

GOSWAMI, Pratik (356 Indie, domácí), Martin BARTAS, Matej LEXA (703 Slovensko, domácí), Natália BOHÁLOVÁ (703 Slovensko, domácí), Adriana VOLNÁ, Jiří ČERVEŇ, Veronika ČERVEŇOVÁ, Petr PEČINKA, Vladimír ŠPUNDA, Miroslav FOJTA a Václav BRÁZDA

Vydání

Briefings in Bioinformatics, Oxford, Oxford University Press, 2021, 1467-5463

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 13.994

Kód RIV

RIV/00216224:14310/21:00121025

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1093/bib/bbaa385

UT WoS

000642298000058

Klíčová slova anglicky

SARS-CoV-2; inverted repeats; CpG methylation; hot spot

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 6. 9. 2023 16:34, doc. Ing. Matej Lexa, Ph.D.

Anotace

V originále

SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 genome. In this study, we inspected high-frequency mutations of SARS-CoV-2 and carried out systematic analyses of their overlay with inverted repeat (IR) loci and CpG islands. The main conclusion of our study is that SARS-CoV-2 hot-spot mutations are significantly enriched within both IRs and CpG island loci. This points to their role in genomic instability and may predict further mutational drive of the SARS-CoV-2 genome. Moreover, CpG islands are strongly enriched upstream from viral ORFs and thus could play important roles in transcription and the viral life cycle. We hypothesize that hypermethylation of these loci will decrease the transcription of viral ORFs and could therefore limit the progression of the disease.

Citovat

GOSWAMI, Pratik, Martin BARTAS, Matej LEXA, Natália BOHÁLOVÁ, Adriana VOLNÁ, Jiří ČERVEŇ, Veronika ČERVEŇOVÁ, Petr PEČINKA, Vladimír ŠPUNDA, Miroslav FOJTA a Václav BRÁZDA. SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci. Briefings in Bioinformatics. Oxford: Oxford University Press, 2021, roč. 22, č. 2, s. 1338-1345. ISSN 1467-5463. Dostupné z: https://dx.doi.org/10.1093/bib/bbaa385.

@article{1733856,
   author = {Goswami, Pratik and Bartas, Martin and Lexa, Matej and Bohálová, Natália and Volná, Adriana and Červeň, Jiří and Červeňová, Veronika and Pečinka, Petr and Špunda, Vladimír and Fojta, Miroslav and Brázda, Václav},
   article_location = {Oxford},
   article_number = {2},
   doi = {http://dx.doi.org/10.1093/bib/bbaa385},
   keywords = {SARS-CoV-2; inverted repeats; CpG methylation; hot spot},
   language = {eng},
   issn = {1467-5463},
   journal = {Briefings in Bioinformatics},
   title = {SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci},
   url = {https://doi.org/10.1093/bib/bbaa385},
   volume = {22},
   year = {2021}
}

TY  - JOUR
ID  - 1733856
AU  - Goswami, Pratik - Bartas, Martin - Lexa, Matej - Bohálová, Natália - Volná, Adriana - Červeň, Jiří - Červeňová, Veronika - Pečinka, Petr - Špunda, Vladimír - Fojta, Miroslav - Brázda, Václav
PY  - 2021
TI  - SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci
JF  - Briefings in Bioinformatics
VL  - 22
IS  - 2
SP  - 1338-1345
EP  - 1338-1345
PB  - Oxford University Press
SN  - 14675463
KW  - SARS-CoV-2
KW  - inverted repeats
KW  - CpG methylation
KW  - hot spot
UR  - https://doi.org/10.1093/bib/bbaa385
L2  - https://doi.org/10.1093/bib/bbaa385
N2  - SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 genome. In this study, we inspected high-frequency mutations of SARS-CoV-2 and carried out systematic analyses of their overlay with inverted repeat (IR) loci and CpG islands. The main conclusion of our study is that SARS-CoV-2 hot-spot mutations are significantly enriched within both IRs and CpG island loci. This points to their role in genomic instability and may predict further mutational drive of the SARS-CoV-2 genome. Moreover, CpG islands are strongly enriched upstream from viral ORFs and thus could play important roles in transcription and the viral life cycle. We hypothesize that hypermethylation of these loci will decrease the transcription of viral ORFs and could therefore limit the progression of the disease.
ER  -

GOSWAMI, Pratik, Martin BARTAS, Matej LEXA, Natália BOHÁLOVÁ, Adriana VOLNÁ, Jiří ČERVEŇ, Veronika ČERVEŇOVÁ, Petr PEČINKA, Vladimír ŠPUNDA, Miroslav FOJTA a Václav BRÁZDA. SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci. \textit{Briefings in Bioinformatics}. Oxford: Oxford University Press, 2021, roč.~22, č.~2, s.~1338-1345. ISSN~1467-5463. Dostupné z: https://dx.doi.org/10.1093/bib/bbaa385.

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