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Verfasst von:Naarmann-de Vries, Isabel S. [VerfasserIn]   i
 Zorbas, Christiane [VerfasserIn]   i
 Lemsara, Amina [VerfasserIn]   i
 Piechotta, Michael [VerfasserIn]   i
 Ernst, Felix Georg Maria [VerfasserIn]   i
 Wacheul, Ludivine [VerfasserIn]   i
 Lafontaine, Denis L. J. [VerfasserIn]   i
 Dieterich, Christoph [VerfasserIn]   i
Titel:Comprehensive identification of diverse ribosomal RNA modifications by targeted nanopore direct RNA sequencing and JACUSA2
Verf.angabe:Isabel S. Naarmann-de Vries, Christiane Zorbas, Amina Lemsara, Michael Piechotta, Felix G. M. Ernst, Ludivine Wacheul, Denis L. J. Lafontaine, Christoph Dieterich
E-Jahr:2023
Jahr:27 Aug 2023
Umfang:14 S.
Fussnoten:Gesehen am 29.11.2023
Titel Quelle:Enthalten in: RNA biology
Ort Quelle:Philadelphia, Pa. : Taylor & Francis, 2004
Jahr Quelle:2023
Band/Heft Quelle:20(2023), 1, Seite 652-665
ISSN Quelle:1555-8584
Abstract:Ribosomal RNAs are decorated by numerous post-transcriptional modifications whose exact roles in ribosome biogenesis, function, and human pathophysiology remain largely unknown. Here, we report a targeted direct rRNA sequencing approach involving a substrate selection step and demonstrate its suitability to identify differential modification sites in combination with the JACUSA2 software. We compared JACUSA2 to other tools designed for RNA modification detection and show that JACUSA2 outperforms other software with regard to detection of base modifications such as methylation, acetylation and aminocarboxypropylation. To illustrate its widespread usability, we applied our method to a collection of CRISPR-Cas9 engineered colon carcinoma cells lacking specific enzymatic activities responsible for particular rRNA modifications and systematically compared them to isogenic wild-type RNAs. Besides the numerous 2′-O methylated riboses and pseudouridylated residues, our approach was suitable to reliably identify differential base methylation and acetylation events. Importantly, our method does not require any prior knowledge of modification sites or the need to train complex models. We further report for the first time detection of human rRNA modifications by direct RNA-sequencing on Flongle flow cells, the smallest-scale nanopore flow cell available to date. The use of these smaller flow cells reduces RNA input requirements, making our workflow suitable for the analysis of samples with limited availability and clinical work.
DOI:doi:10.1080/15476286.2023.2248752
URL:Bitte beachten Sie: Dies ist ein Bibliographieeintrag. Ein Volltextzugriff für Mitglieder der Universität besteht hier nur, falls für die entsprechende Zeitschrift/den entsprechenden Sammelband ein Abonnement besteht oder es sich um einen OpenAccess-Titel handelt.

kostenfrei: Volltext: https://doi.org/10.1080/15476286.2023.2248752
 DOI: https://doi.org/10.1080/15476286.2023.2248752
Datenträger:Online-Ressource
Sprache:eng
Sach-SW:cytidine acetylation
 direct RNA-seq
 nanopore
 ribosomal RNA
 RNA methylation
 RNA modification
K10plus-PPN:1871608155
Verknüpfungen:→ Zeitschrift

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