Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing.
Nat Biotechnol
; 39(10): 1278-1291, 2021 10.
Article
em En
| MEDLINE
| ID: mdl-33986546
ABSTRACT
Nanopore RNA sequencing shows promise as a method for discriminating and identifying different RNA modifications in native RNA. Expanding on the ability of nanopore sequencing to detect N6-methyladenosine, we show that other modifications, in particular pseudouridine (Ψ) and 2'-O-methylation (Nm), also result in characteristic base-calling 'error' signatures in the nanopore data. Focusing on Ψ modification sites, we detected known and uncovered previously unreported Ψ sites in mRNAs, non-coding RNAs and rRNAs, including a Pus4-dependent Ψ modification in yeast mitochondrial rRNA. To explore the dynamics of pseudouridylation, we treated yeast cells with oxidative, cold and heat stresses and detected heat-sensitive Ψ-modified sites in small nuclear RNAs, small nucleolar RNAs and mRNAs. Finally, we developed a software, nanoRMS, that estimates per-site modification stoichiometries by identifying single-molecule reads with altered current intensity and trace profiles. This work demonstrates that Nm and Ψ RNA modifications can be detected in cellular RNAs and that their modification stoichiometry can be quantified by nanopore sequencing of native RNA.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Pseudouridina
/
RNA
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Análise de Sequência de RNA
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Sequenciamento por Nanoporos
Idioma:
En
Ano de publicação:
2021
Tipo de documento:
Article