Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases
RNA editing, a common and potentially highly functional form of RNA modification, encompasses two different RNA modifications, namely adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. As inosines are interpreted as guanosines by the cellular machinery, both A-to-I and C-to-U ed...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2024-03-01
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| Series: | Molecular Therapy: Nucleic Acids |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2162253123003037 |
| _version_ | 1797385193067118592 |
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| author | Korina Karagianni Alessia Bibi Alisia Madé Shubhra Acharya Mikko Parkkonen Teodora Barbalata Prashant K. Srivastava David de Gonzalo-Calvo Constanza Emanueli Fabio Martelli Yvan Devaux Dimitra Dafou A. Yaël Nossent |
| author_facet | Korina Karagianni Alessia Bibi Alisia Madé Shubhra Acharya Mikko Parkkonen Teodora Barbalata Prashant K. Srivastava David de Gonzalo-Calvo Constanza Emanueli Fabio Martelli Yvan Devaux Dimitra Dafou A. Yaël Nossent |
| author_sort | Korina Karagianni |
| collection | DOAJ |
| description | RNA editing, a common and potentially highly functional form of RNA modification, encompasses two different RNA modifications, namely adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. As inosines are interpreted as guanosines by the cellular machinery, both A-to-I and C-to-U editing change the nucleotide sequence of the RNA. Editing events in coding sequences have the potential to change the amino acid sequence of proteins, whereas editing events in noncoding RNAs can, for example, affect microRNA target binding. With advancing RNA sequencing technology, more RNA editing events are being discovered, studied, and reported. However, RNA editing events are still often overlooked or discarded as sequence read quality defects. With this position paper, we aim to provide guidelines and recommendations for the detection, validation, and follow-up experiments to study RNA editing, taking examples from the fields of cardiovascular and brain disease. We discuss all steps, from sample collection, storage, and preparation, to different strategies for RNA sequencing and editing-sensitive data analysis strategies, to validation and follow-up experiments, as well as potential pitfalls and gaps in the available technologies. This paper may be used as an experimental guideline for RNA editing studies in any disease context. |
| first_indexed | 2024-03-08T21:50:37Z |
| format | Article |
| id | doaj.art-02ae5e2b9de447f4986105af97021dfe |
| institution | Directory Open Access Journal |
| issn | 2162-2531 |
| language | English |
| last_indexed | 2024-03-08T21:50:37Z |
| publishDate | 2024-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Molecular Therapy: Nucleic Acids |
| spelling | doaj.art-02ae5e2b9de447f4986105af97021dfe2023-12-20T07:34:15ZengElsevierMolecular Therapy: Nucleic Acids2162-25312024-03-01351102085Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseasesKorina Karagianni0Alessia Bibi1Alisia Madé2Shubhra Acharya3Mikko Parkkonen4Teodora Barbalata5Prashant K. Srivastava6David de Gonzalo-Calvo7Constanza Emanueli8Fabio Martelli9Yvan Devaux10Dimitra Dafou11A. Yaël Nossent12Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, GreeceMolecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy; Department of Biosciences, University of Milan, Milan, ItalyMolecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, ItalyCardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-alzette, LuxembourgResearch Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, FinlandLipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8, B. P. Hasdeu Street, 050568 Bucharest, RomaniaNational Heart & Lung Institute, Imperial College London, London, UKTranslational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain; CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, SpainNational Heart & Lung Institute, Imperial College London, London, UKMolecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, ItalyCardiovascular Research Unit, Luxembourg Institute of Health, Strassen, LuxembourgDepartment of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, GreeceDepartment of Surgery, Leiden University Medical Center, Leiden, the Netherlands; Department of Nutrition, Exercise and Sports (NEXS), University of Copenhagen, Copenhagen, Denmark; Corresponding author: A. Yaël Nossent, Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands.RNA editing, a common and potentially highly functional form of RNA modification, encompasses two different RNA modifications, namely adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. As inosines are interpreted as guanosines by the cellular machinery, both A-to-I and C-to-U editing change the nucleotide sequence of the RNA. Editing events in coding sequences have the potential to change the amino acid sequence of proteins, whereas editing events in noncoding RNAs can, for example, affect microRNA target binding. With advancing RNA sequencing technology, more RNA editing events are being discovered, studied, and reported. However, RNA editing events are still often overlooked or discarded as sequence read quality defects. With this position paper, we aim to provide guidelines and recommendations for the detection, validation, and follow-up experiments to study RNA editing, taking examples from the fields of cardiovascular and brain disease. We discuss all steps, from sample collection, storage, and preparation, to different strategies for RNA sequencing and editing-sensitive data analysis strategies, to validation and follow-up experiments, as well as potential pitfalls and gaps in the available technologies. This paper may be used as an experimental guideline for RNA editing studies in any disease context.http://www.sciencedirect.com/science/article/pii/S2162253123003037MT: RNA/DNA editingRNA editingA-to-I editingC-to-U editingmethodologycardiovascular disease |
| spellingShingle | Korina Karagianni Alessia Bibi Alisia Madé Shubhra Acharya Mikko Parkkonen Teodora Barbalata Prashant K. Srivastava David de Gonzalo-Calvo Constanza Emanueli Fabio Martelli Yvan Devaux Dimitra Dafou A. Yaël Nossent Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases Molecular Therapy: Nucleic Acids MT: RNA/DNA editing RNA editing A-to-I editing C-to-U editing methodology cardiovascular disease |
| title | Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases |
| title_full | Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases |
| title_fullStr | Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases |
| title_full_unstemmed | Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases |
| title_short | Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases |
| title_sort | recommendations for detection validation and evaluation of rna editing events in cardiovascular and neurological neurodegenerative diseases |
| topic | MT: RNA/DNA editing RNA editing A-to-I editing C-to-U editing methodology cardiovascular disease |
| url | http://www.sciencedirect.com/science/article/pii/S2162253123003037 |
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