دورية أكاديمية
Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing.
العنوان: | Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing. |
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المؤلفون: | Begik O; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.; Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.; UNSW Sydney, Kensington, NSW, Australia., Lucas MC; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain., Pryszcz LP; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.; International Institute of Molecular and Cell Biology, Warsaw, Poland., Ramirez JM; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain., Medina R; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain., Milenkovic I; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain., Cruciani S; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain., Liu H; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain., Vieira HGS; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain., Sas-Chen A; Weizmann Institute of Science, Rehovot, Israel., Mattick JS; UNSW Sydney, Kensington, NSW, Australia., Schwartz S; Weizmann Institute of Science, Rehovot, Israel., Novoa EM; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. eva.novoa@crg.eu.; Universitat Pompeu Fabra (UPF), Barcelona, Spain. eva.novoa@crg.eu. |
المصدر: | Nature biotechnology [Nat Biotechnol] 2021 Oct; Vol. 39 (10), pp. 1278-1291. Date of Electronic Publication: 2021 May 13. |
نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
اللغة: | English |
بيانات الدورية: | Publisher: Nature America Publishing Country of Publication: United States NLM ID: 9604648 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1546-1696 (Electronic) Linking ISSN: 10870156 NLM ISO Abbreviation: Nat Biotechnol Subsets: MEDLINE |
أسماء مطبوعة: | Publication: New York Ny : Nature America Publishing Original Publication: New York, NY : Nature Pub. Co., [1996- |
مواضيع طبية MeSH: | Nanopore Sequencing/*methods , Pseudouridine/*metabolism , RNA/*metabolism , Sequence Analysis, RNA/*methods, Algorithms ; Gene Expression Profiling ; Intramolecular Transferases/metabolism ; Mitochondria/genetics ; Pseudouridine/genetics ; RNA/genetics ; RNA Processing, Post-Transcriptional/genetics ; RNA, Fungal/genetics ; RNA, Fungal/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Ribosomal/genetics ; RNA, Ribosomal/metabolism ; Saccharomyces cerevisiae/genetics ; Software ; Stress, Physiological/genetics |
مستخلص: | 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 N 6 -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. (© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.) |
التعليقات: | Comment in: Nat Methods. 2021 Jul;18(7):711. (PMID: 34239099) |
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المشرفين على المادة: | 0 (RNA, Fungal) 0 (RNA, Messenger) 0 (RNA, Ribosomal) 1445-07-4 (Pseudouridine) 63231-63-0 (RNA) EC 5.4.- (Intramolecular Transferases) EC 5.4.99.12 (tRNA-pseudouridine synthase I) |
تواريخ الأحداث: | Date Created: 20210514 Date Completed: 20211116 Latest Revision: 20220630 |
رمز التحديث: | 20231215 |
DOI: | 10.1038/s41587-021-00915-6 |
PMID: | 33986546 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1546-1696 |
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DOI: | 10.1038/s41587-021-00915-6 |