Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling

Pseudouridine (Ψ) is an abundant mRNA modification in mammalian transcriptome, but its functions have remained elusive due to the difficulty of transcriptome-wide mapping. We develop a nanopore native RNA sequencing method for quantitative Ψ prediction (NanoPsu) that utilizes native content training...

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Autores principales: Huang, Sihao, Zhang, Wen, Katanski, Christopher D., Dersh, Devin, Dai, Qing, Lolans, Karen, Yewdell, Jonathan, Eren, A. Murat, Pan, Tao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Short Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8646010/
https://www.ncbi.nlm.nih.gov/pubmed/34872593
http://dx.doi.org/10.1186/s13059-021-02557-y
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author Huang, Sihao
Zhang, Wen
Katanski, Christopher D.
Dersh, Devin
Dai, Qing
Lolans, Karen
Yewdell, Jonathan
Eren, A. Murat
Pan, Tao
author_facet Huang, Sihao
Zhang, Wen
Katanski, Christopher D.
Dersh, Devin
Dai, Qing
Lolans, Karen
Yewdell, Jonathan
Eren, A. Murat
Pan, Tao
author_sort Huang, Sihao
collection PubMed
description Pseudouridine (Ψ) is an abundant mRNA modification in mammalian transcriptome, but its functions have remained elusive due to the difficulty of transcriptome-wide mapping. We develop a nanopore native RNA sequencing method for quantitative Ψ prediction (NanoPsu) that utilizes native content training, machine learning modeling, and single-read linkage analysis. Biologically, we find interferon inducible Ψ modifications in interferon-stimulated gene transcripts which are consistent with a role of Ψ in enabling efficacy of mRNA vaccines. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02557-y.
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spelling pubmed-86460102021-12-06 Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling Huang, Sihao Zhang, Wen Katanski, Christopher D. Dersh, Devin Dai, Qing Lolans, Karen Yewdell, Jonathan Eren, A. Murat Pan, Tao Genome Biol Short Report Pseudouridine (Ψ) is an abundant mRNA modification in mammalian transcriptome, but its functions have remained elusive due to the difficulty of transcriptome-wide mapping. We develop a nanopore native RNA sequencing method for quantitative Ψ prediction (NanoPsu) that utilizes native content training, machine learning modeling, and single-read linkage analysis. Biologically, we find interferon inducible Ψ modifications in interferon-stimulated gene transcripts which are consistent with a role of Ψ in enabling efficacy of mRNA vaccines. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02557-y. BioMed Central 2021-12-06 /pmc/articles/PMC8646010/ /pubmed/34872593 http://dx.doi.org/10.1186/s13059-021-02557-y Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Short Report
Huang, Sihao
Zhang, Wen
Katanski, Christopher D.
Dersh, Devin
Dai, Qing
Lolans, Karen
Yewdell, Jonathan
Eren, A. Murat
Pan, Tao
Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling
title Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling
title_full Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling
title_fullStr Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling
title_full_unstemmed Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling
title_short Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling
title_sort interferon inducible pseudouridine modification in human mrna by quantitative nanopore profiling
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8646010/
https://www.ncbi.nlm.nih.gov/pubmed/34872593
http://dx.doi.org/10.1186/s13059-021-02557-y
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