Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants

The causative agent of COVID-19 pandemic, SARS-CoV-2, has a 29,903 bases positive-sense single-stranded RNA genome. RNAs exhibit about 150 modified bases that are essential for proper function. Among internal modified bases, the <i>N<sup>6</sup></i>-methyladenosine, or m6A, i...

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Autores principales:	João H. C. Campos, Juliana T. Maricato, Carla T. Braconi, Fernando Antoneli, Luiz Mario R. Janini, Marcelo R. S. Briones
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	SARS-CoV-2 COVID-19 m6A direct RNA sequencing RNA methylation Epitranscriptomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/e19471fc1b8c4cc08aa062c078f2f833
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spelling	oai:doaj.org-article:e19471fc1b8c4cc08aa062c078f2f8332021-11-25T19:12:18ZDirect RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants10.3390/v131121081999-4915https://doaj.org/article/e19471fc1b8c4cc08aa062c078f2f8332021-10-01T00:00:00Zhttps://www.mdpi.com/1999-4915/13/11/2108https://doaj.org/toc/1999-4915The causative agent of COVID-19 pandemic, SARS-CoV-2, has a 29,903 bases positive-sense single-stranded RNA genome. RNAs exhibit about 150 modified bases that are essential for proper function. Among internal modified bases, the <i>N<sup>6</sup></i>-methyladenosine, or m6A, is the most frequent, and is implicated in SARS-CoV-2 immune response evasion. Although the SARS-CoV-2 genome is RNA, almost all genomes sequenced thus far are, in fact, reverse transcribed complementary DNAs. This process reduces the true complexity of these viral genomes because the incorporation of dNTPs hides RNA base modifications. Here, we present an initial exploration of Nanopore direct RNA sequencing to assess the m6A residues in the SARS-CoV-2 sequences of ORF3a, E, M, ORF6, ORF7a, ORF7b, ORF8, N, ORF10 and the 3′-untranslated region. We identified fifteen m6A methylated positions, of which, six are in ORF N. Additionally, because m6A is associated with the DRACH motif, we compared its distribution in major SARS-CoV-2 variants. Although DRACH is highly conserved among variants, we show that variants Beta and Eta have a fourth position C > U change in DRACH at 28,884b that could affect methylation. This is the first report of direct RNA sequencing of a Brazilian SARS-CoV-2 sample coupled with the identification of modified bases.João H. C. CamposJuliana T. MaricatoCarla T. BraconiFernando AntoneliLuiz Mario R. JaniniMarcelo R. S. BrionesMDPI AGarticleSARS-CoV-2COVID-19m6Adirect RNA sequencingRNA methylationEpitranscriptomicsMicrobiologyQR1-502ENViruses, Vol 13, Iss 2108, p 2108 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	SARS-CoV-2 COVID-19 m6A direct RNA sequencing RNA methylation Epitranscriptomics Microbiology QR1-502
spellingShingle	SARS-CoV-2 COVID-19 m6A direct RNA sequencing RNA methylation Epitranscriptomics Microbiology QR1-502 João H. C. Campos Juliana T. Maricato Carla T. Braconi Fernando Antoneli Luiz Mario R. Janini Marcelo R. S. Briones Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants
description	The causative agent of COVID-19 pandemic, SARS-CoV-2, has a 29,903 bases positive-sense single-stranded RNA genome. RNAs exhibit about 150 modified bases that are essential for proper function. Among internal modified bases, the <i>N<sup>6</sup></i>-methyladenosine, or m6A, is the most frequent, and is implicated in SARS-CoV-2 immune response evasion. Although the SARS-CoV-2 genome is RNA, almost all genomes sequenced thus far are, in fact, reverse transcribed complementary DNAs. This process reduces the true complexity of these viral genomes because the incorporation of dNTPs hides RNA base modifications. Here, we present an initial exploration of Nanopore direct RNA sequencing to assess the m6A residues in the SARS-CoV-2 sequences of ORF3a, E, M, ORF6, ORF7a, ORF7b, ORF8, N, ORF10 and the 3′-untranslated region. We identified fifteen m6A methylated positions, of which, six are in ORF N. Additionally, because m6A is associated with the DRACH motif, we compared its distribution in major SARS-CoV-2 variants. Although DRACH is highly conserved among variants, we show that variants Beta and Eta have a fourth position C > U change in DRACH at 28,884b that could affect methylation. This is the first report of direct RNA sequencing of a Brazilian SARS-CoV-2 sample coupled with the identification of modified bases.
format	article
author	João H. C. Campos Juliana T. Maricato Carla T. Braconi Fernando Antoneli Luiz Mario R. Janini Marcelo R. S. Briones
author_facet	João H. C. Campos Juliana T. Maricato Carla T. Braconi Fernando Antoneli Luiz Mario R. Janini Marcelo R. S. Briones
author_sort	João H. C. Campos
title	Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants
title_short	Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants
title_full	Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants
title_fullStr	Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants
title_full_unstemmed	Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants
title_sort	direct rna sequencing reveals sars-cov-2 m6a sites and possible differential drach motif methylation among variants
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/e19471fc1b8c4cc08aa062c078f2f833
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Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants

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