Surpassing limits of static RNA modification analysis with dynamic NAIL-MS
Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved..
Ribonucleic acids (RNA) are extensively modified. These modifications are quantified by mass spectrometry (LC-MS/MS) to determine the abundance of a modification under certain conditions or in various genetic backgrounds. With LC-MS/MS the steady state of modifications is determined, and thus we only have a static view of the dynamics of RNA modifications. With nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) we overcome this limitation and get access to the dynamics of RNA modifications. We describe labeling techniques for E. coli, S. cerevisiae and human cell culture and the current instrumental limitations. We present the power of NAIL-MS but we also outline validation experiments, which are necessary for correct data interpretation. As an example, we apply NAIL-MS to study the demethylation of adenine and cytidine, which are methylated by the damaging agent methyl-methanesulfonate in E. coli. With NAIL-MS we exclude the concurrent processes for removal of RNA methylation, namely RNA degradation, turnover and dilution. We use our tool to study the speed and efficiency of 1-methyladenosine and 3-methylcytidine demethylation. We further outline current limitations of NAIL-MS but also potential future uses for e.g. relative quantification of tRNA isoacceptor abundances.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2019 |
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| Erschienen: |
2019 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:156 |
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| Enthalten in: |
Methods (San Diego, Calif.) - 156(2019) vom: 01. März, Seite 91-101 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Reichle, Valentin F [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 20.11.2019 Date Revised 10.12.2019 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1016/j.ymeth.2018.10.025 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM290292298 |
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| 100 | 1 | |a Reichle, Valentin F |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Surpassing limits of static RNA modification analysis with dynamic NAIL-MS |
| 264 | 1 | |c 2019 | |
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| 500 | |a Date Revised 10.12.2019 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved. | ||
| 520 | |a Ribonucleic acids (RNA) are extensively modified. These modifications are quantified by mass spectrometry (LC-MS/MS) to determine the abundance of a modification under certain conditions or in various genetic backgrounds. With LC-MS/MS the steady state of modifications is determined, and thus we only have a static view of the dynamics of RNA modifications. With nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) we overcome this limitation and get access to the dynamics of RNA modifications. We describe labeling techniques for E. coli, S. cerevisiae and human cell culture and the current instrumental limitations. We present the power of NAIL-MS but we also outline validation experiments, which are necessary for correct data interpretation. As an example, we apply NAIL-MS to study the demethylation of adenine and cytidine, which are methylated by the damaging agent methyl-methanesulfonate in E. coli. With NAIL-MS we exclude the concurrent processes for removal of RNA methylation, namely RNA degradation, turnover and dilution. We use our tool to study the speed and efficiency of 1-methyladenosine and 3-methylcytidine demethylation. We further outline current limitations of NAIL-MS but also potential future uses for e.g. relative quantification of tRNA isoacceptor abundances | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Validation Study | |
| 650 | 4 | |a Demethylation | |
| 650 | 4 | |a Epitranscriptome | |
| 650 | 4 | |a LC-MS/MS | |
| 650 | 4 | |a Nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS) | |
| 650 | 4 | |a tRNA damage repair | |
| 650 | 4 | |a tRNA modification | |
| 650 | 7 | |a Carbon Isotopes |2 NLM | |
| 650 | 7 | |a Nitrogen Isotopes |2 NLM | |
| 650 | 7 | |a RNA, Messenger |2 NLM | |
| 650 | 7 | |a 1-methyladenosine |2 NLM | |
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| 650 | 7 | |a RNA, Transfer |2 NLM | |
| 650 | 7 | |a 9014-25-9 |2 NLM | |
| 650 | 7 | |a Methyl Methanesulfonate |2 NLM | |
| 650 | 7 | |a AT5C31J09G |2 NLM | |
| 650 | 7 | |a Adenosine |2 NLM | |
| 650 | 7 | |a K72T3FS567 |2 NLM | |
| 700 | 1 | |a Kaiser, Steffen |e verfasserin |4 aut | |
| 700 | 1 | |a Heiss, Matthias |e verfasserin |4 aut | |
| 700 | 1 | |a Hagelskamp, Felix |e verfasserin |4 aut | |
| 700 | 1 | |a Borland, Kayla |e verfasserin |4 aut | |
| 700 | 1 | |a Kellner, Stefanie |e verfasserin |4 aut | |
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