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

Autor(es)

Campos, Joao H. C. ^[1] ; Maricato, Juliana T. ^[2] ; Braconi, Carla T. ^[2] ; Antoneli, Fernando ^[1] ; Janini, Luiz Mario R. ^[2] ; Briones, Marcelo R. S. ^[1]

Afiliação do(s) autor(es)

^[1] Fed Univ Sao Paulo UNIFESP, Ctr Med Bioinformat, Escola Paulista Med, BR-04039032 Sao Paulo - Brazil

^[2] Fed Univ Sao Paulo UNIFESP, Dept Microbiol Immunol & Parasitol, Escola Paulista Med, BR-04023062 Sao Paulo - Brazil

• Tipo de documento: Artigo Científico
• Fonte: Viruses-Basel; v. 13, n. 11 NOV 2021.
• Citações Web of Science: 0

Resumo

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 N-6-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 \& PRIME;-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. (AU)

• Processo FAPESP: 20/08943-5 - Investigação de elementos induzidos pela resposta vacinal nos indivíduos submetidos aos testes clínicos com a vacina ChAdOx1 nCOV-19
• Beneficiário: Luiz Mário Ramos Janini
• Modalidade de apoio: Auxílio à Pesquisa - Temático