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Tytuł:
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Long-read single-molecule RNA structure sequencing using nanopore.
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Autorzy:
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Bizuayehu TT; Computational Biology Unit, Department of Informatics, University of Bergen, Norway.; Sars International Center for Marine Molecular Biology, University of Bergen, Norway.
Labun K; Computational Biology Unit, Department of Informatics, University of Bergen, Norway.
Jakubec M; Department of Chemistry, University of Tromsø, Norway.
Jefimov K; Computational Biology Unit, Department of Informatics, University of Bergen, Norway.
Niazi AM; Computational Biology Unit, Department of Informatics, University of Bergen, Norway.
Valen E; Computational Biology Unit, Department of Informatics, University of Bergen, Norway.; Sars International Center for Marine Molecular Biology, University of Bergen, Norway.
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Źródło:
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Nucleic acids research [Nucleic Acids Res] 2022 Nov 11; Vol. 50 (20), pp. e120.
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Typ publikacji:
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Journal Article; Research Support, Non-U.S. Gov't
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Język:
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English
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Imprint Name(s):
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Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
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MeSH Terms:
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Nanopores*
RNA*/genetics
RNA*/chemistry
Sequence Analysis, RNA*/methods
Nucleic Acid Conformation*
Riboswitch ; Transcriptome
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References:
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Nat Protoc. 2015 Nov;10(11):1643-69. (PMID: 26426499)
Algorithms Mol Biol. 2011 Nov 24;6:26. (PMID: 22115189)
J Mol Biol. 1986 Oct 5;191(3):483-93. (PMID: 2434656)
J Mol Biol. 1984 Nov 25;180(1):151-77. (PMID: 6210372)
Proc Natl Acad Sci U S A. 2013 Mar 12;110(11):4188-93. (PMID: 23440214)
Nat Biotechnol. 2021 Mar;39(3):336-346. (PMID: 33106685)
J Mol Biol. 1991 Sep 5;221(1):293-308. (PMID: 1717695)
Nature. 2014 Jan 30;505(7485):701-5. (PMID: 24336214)
Biochemistry. 2017 Sep 5;56(35):4713-4721. (PMID: 28820243)
Nat Rev Genet. 2018 Oct;19(10):615-634. (PMID: 30054568)
Nucleic Acids Res. 2019 Jan 8;47(D1):D1250-D1251. (PMID: 30535383)
Biochemistry. 1971 Aug 31;10(18):3335-42. (PMID: 5118618)
Nucleic Acids Res. 2011 Oct;39(19):8586-98. (PMID: 21745821)
Nature. 2006 Jun 29;441(7097):1167-71. (PMID: 16728979)
Nature. 2010 Sep 2;467(7311):103-7. (PMID: 20811459)
Proc Natl Acad Sci U S A. 2014 Sep 23;111(38):13858-63. (PMID: 25205807)
Nat Methods. 2014 Sep;11(9):959-65. (PMID: 25028896)
Biochemistry. 2019 Jun 11;58(23):2655-2664. (PMID: 31117385)
Cell. 2001 Oct 5;107(1):103-14. (PMID: 11595189)
Nucleic Acids Res. 2021 Jan 8;49(D1):D212-D220. (PMID: 33106848)
Nat Rev Mol Cell Biol. 2018 Mar;19(3):158-174. (PMID: 29165424)
Nat Protoc. 2016 Feb;11(2):273-90. (PMID: 26766114)
Nature. 2009 Mar 12;458(7235):233-7. (PMID: 19169240)
Nature. 2002 Oct 31;419(6910):952-6. (PMID: 12410317)
J Mol Biol. 2002 Apr 5;317(4):507-21. (PMID: 11955006)
Nat Methods. 2021 Mar;18(3):249-252. (PMID: 33619392)
Nat Chem Biol. 2013 Jan;9(1):18-20. (PMID: 23178934)
Biochemistry. 1988 Jan 26;27(2):582-92. (PMID: 3349049)
Proc Natl Acad Sci U S A. 1980 Aug;77(8):4679-82. (PMID: 6159633)
Nature. 2020 Jun;582(7812):438-442. (PMID: 32555469)
Cell Genom. 2022 Feb 9;2(2):. (PMID: 35252946)
Bioinformatics. 2018 Sep 15;34(18):3094-3100. (PMID: 29750242)
J Biol Chem. 2008 Jul 4;283(27):19011-25. (PMID: 18460470)
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Substance Nomenclature:
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0 (Riboswitch)
63231-63-0 (RNA)
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Entry Date(s):
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Date Created: 20220927 Date Completed: 20221212 Latest Revision: 20221223
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Update Code:
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20240105
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PubMed Central ID:
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PMC9723614
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DOI:
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10.1093/nar/gkac775
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PMID:
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36166000
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RNA molecules can form secondary and tertiary structures that can regulate their localization and function. Using enzymatic or chemical probing together with high-throughput sequencing, secondary structure can be mapped across the entire transcriptome. However, a limiting factor is that only population averages can be obtained since each read is an independent measurement. Although long-read sequencing has recently been used to determine RNA structure, these methods still used aggregate signals across the strands to detect structure. Averaging across the population also means that only limited information about structural heterogeneity across molecules or dependencies within each molecule can be obtained. Here, we present Single-Molecule Structure sequencing (SMS-seq) that combines structural probing with native RNA sequencing to provide non-amplified, structural profiles of individual molecules with novel analysis methods. Our new approach using mutual information enabled single molecule structural interrogation. Each RNA is probed at numerous bases enabling the discovery of dependencies and heterogeneity of structural features. We also show that SMS-seq can capture tertiary interactions, dynamics of riboswitch ligand binding, and mRNA structural features.
(© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)