دورية أكاديمية
Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing.
| العنوان: | Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. |
|---|---|
| المؤلفون: | Lucas MC; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain., Pryszcz LP; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain., Medina R; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain., Milenkovic I; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain., Camacho N; Institute for Research in Biomedicine (IRB), Barcelona, Spain., Marchand V; CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France., Motorin Y; CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France., Ribas de Pouplana L; Institute for Research in Biomedicine (IRB), Barcelona, Spain.; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain., Novoa EM; Centre for Genomic Regulation (CRG), 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] 2024 Jan; Vol. 42 (1), pp. 72-86. Date of Electronic Publication: 2023 Apr 06. |
| نوع المنشور: | Journal Article |
| 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* , Nanopores*, RNA ; RNA, Transfer/chemistry ; Sequence Analysis, RNA/methods |
| مستخلص: | Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both tRNA abundances and modification dynamics in a single experiment. We show that default nanopore sequencing settings discard the vast majority of tRNA reads, leading to poor sequencing yields and biased representations of tRNA abundances based on their transcript length. Re-processing of raw nanopore current intensity signals leads to a 12-fold increase in the number of recovered tRNA reads and enables recapitulation of accurate tRNA abundances. We then apply Nano-tRNAseq to Saccharomyces cerevisiae tRNA populations, revealing crosstalks and interdependencies between different tRNA modification types within the same molecule and changes in tRNA populations in response to oxidative stress. (© 2023. The Author(s).) |
| التعليقات: | Comment in: Nat Genet. 2023 May;55(5):727. (PMID: 37173525) |
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| المشرفين على المادة: | 63231-63-0 (RNA) 9014-25-9 (RNA, Transfer) |
| تواريخ الأحداث: | Date Created: 20230406 Date Completed: 20240118 Latest Revision: 20240119 |
| رمز التحديث: | 20240119 |
| مُعرف محوري في PubMed: | PMC10791586 |
| DOI: | 10.1038/s41587-023-01743-6 |
| PMID: | 37024678 |
| قاعدة البيانات: | MEDLINE |
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| DOI: | 10.1038/s41587-023-01743-6 |