2024
DOI: 10.1101/2024.01.31.578250
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Integrative analysis of nanopore direct RNA sequencing data reveals a role of PUS7-dependent pseudouridylation in regulation of m6A and m5C modifications

Mohit Bansal,
Anirban Kundu,
Anamika Gupta
et al.

Abstract: Pseudouridylation is a prevalent post-transcriptional RNA modification that impacts many aspects of RNA biology and function. The conversion of uridine to pseudouridine (ψ) is catalyzed by the family of pseudouridine synthases (PUSs). Development of robust methods to determine PUS-dependent regulation of ψ location and stoichiometry in low abundant mRNA is essential for biological and functional understanding of pseudouridylation. Here, we present a framework, NanoPsiPy, for identifying ψ sites and quantify th… Show more

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“…Long-read sequencing enables accurate mapping of diverse RNA features with transcript isoform resolution. Such features include, among others, chemical modifications (Acera Mateos et al, 2024;Bansal et al, 2024;Liu et al, 2019;Stephenson et al, 2020), structured regions (Aw et al, 2021;Stephenson et al, 2022), and RNA-protein interacting sites (Lin et al, 2022). The functional roles of these RNA features are often linked to their position relative to transcript landmarks, such as transcription start sites, splice junctions, start and stop codons, and polyadenylation sites.…”
Section: Introductionmentioning
confidence: 99%
“…Long-read sequencing enables accurate mapping of diverse RNA features with transcript isoform resolution. Such features include, among others, chemical modifications (Acera Mateos et al, 2024;Bansal et al, 2024;Liu et al, 2019;Stephenson et al, 2020), structured regions (Aw et al, 2021;Stephenson et al, 2022), and RNA-protein interacting sites (Lin et al, 2022). The functional roles of these RNA features are often linked to their position relative to transcript landmarks, such as transcription start sites, splice junctions, start and stop codons, and polyadenylation sites.…”
Section: Introductionmentioning
confidence: 99%