RNA Modifications: Methods and Protocols

ISBN-13: 9781071613764 / Angielski / Miękka / 2022

McMahon, Mary

Opis

This detailed book describes some of the most recent advances and up-to-date methodologies to detect, quantify, analyze, and elucidate the biological function of different types of RNA modifications. Importantly, the methodologies and tools described herein can be applied to a wide variety of organisms and can be used to address biological and clinical questions. Beginning with a section on bioinformatics tools, the collection continues with sections on detecting RNA modifications using Nanopore direct RNA sequencing, next-generation sequencing approaches, qPCR- and molecular biology-based methods, mass spectrometry- and NMR-based methods, as well as approaches to assess kinetics, determinants, and functions of RNA modifications. Written for the highly successful Methods in Molecular Biology series style, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, RNA Modifications: Methods and Protocols serves as an ideal guide for those working directly in the fields of epitranscriptomics and post-transcriptional gene regulation, as well as for scientists and clinicians interested in bioinformatic tools to study RNA modifications and techniques to dissect their roles in physiology and disease.

Chapter 20 is available open access under a CC BY 4.0 license.

Spis treści

Part I: Bioinformatic Tools to Study RNA Modifications

 

1. RNA Post-Transcriptional Modification Mapping Data Analysis Using RNA Framework

            Ilaria Manfredonia and Danny Incarnato

 

2. An Informatics Pipeline for Profiling and Annotating RNA Modifications

            Qi Liu, Xiaoqiang Lang, and Richard I. Gregory

 

Part II: Detecting RNA Modifications Using Nanopore Direct RNA Sequencing

 

3. EpiNano: Detection of m⁶A RNA Modifications Using Oxford Nanopore Direct RNA Sequencing

            Huanle Liu, Oguzhan Begik, and Eva Maria Novoa

 

4. Adaptation of Human Ribosomal RNA for Nanopore Sequencing of Canonical and Modified Nucleotides

            Miten Jain, Hugh E. Olsen, Mark Akeson, and Robin Abu-Shumays

 

Part III: Next-Generation Sequencing Approaches to Detect and Capture Modified RNAs

 

5. AlkAniline-Seq: A Highly Sensitive and Specific Method for Simultaneous Mapping of 7-Methyl-Guanosine (m⁷G) and 3-Methyl-Cytidine (m³C) in RNAs by High-Throughput Sequencing

            Virginie Marchand, Lilia Ayadi, Valérie Bourguignon-Igel, Mark Helm, and Yuri Motorin

 

6. Transcriptome-Wide Detection of Internal N⁷-Methylguanosine

            Li-Sheng Zhang, Chang Liu, and Chuan He

 

7. miCLIP-MaPseq Identifies Substrates of Radical SAM RNA Methylating Enzyme Using Mechanistic Crosslinking and Mismatch Profiling

            Vanja Stojković, David E. Weinberg, and Danica Galonić Fujimori

 

8. Mapping RNA Modifications Using Photo-Crosslinking-Assisted Modification Sequencing

            Bryan R. Cullen and Kevin Tsai

 

9. Quantitative and Single Nucleotide Resolution Profiling of RNA 5-Methylcytosine

            Jun Li, Xingyu Wu, Trung Do, Vy Nguyen, Jing Zhao, Pei Qin Ng, Alice Burgess, Rakesh David, and Iain Searle

 

10. A Small RNA-Seq Protocol with Less Bias and Improved Capture of 2’-O-Methyl RNAs

            Erwin L. van Dijk and Claude Thermes

 

Part IV: Assessing RNA Modifications Using qPCR- and Molecular Biology-Based Methods

 

11. Assessing 2'-O-Methylation of mRNA Using Quantitative PCR

            Brittany A. Elliott and Christopher L. Holley

 

12. Relative Quantification of Residue Specific m6A RNA Methylation Using m6A-RT-QPCR

            Ane Olazagoitia-Garmendia and Ainara Castellanos-Rubio

 

13. Monitoring the 5-Methoxycarbonylmethyl-2-Thiouridine (mcm5s2U) Modification Utilizing the Gamma-Toxin Endonuclease

            Jenna M. Lentini and Dragony Fu

 

14. Analysis of Queuosine tRNA Modifications Using APB Northern Blot Assays

            Cansu Cirzi and Francesca Tuorto

 

15. Detecting ADP-Ribosylation in RNA

            Deeksha Munnur and Ivan Ahel

 

Part V: Mass Spectrometry- and NMR-Based Methods for RNA Modifications Analysis

 

16. Detecting Internal N7-Methylguanosine mRNA Modifications by Differential Enzymatic Digestion Coupled with Mass Spectrometry Analysis

            Xue-Jiao You and Bi-Feng Yuan

 

17. A General LC-MS-Based Method for Direct and De Novo Sequencing of RNA Mixtures Containing Both Canonical and Modified Nucleotides

            Ning Zhang, Shundi Shi, Xiaohong Yuan, Wenhao Ni, Xuanting Wang, Barney Yoo, Tony Z. Jia, Wenjia Li, and Shenglong Zhang

 

18. Quantification of Modified Nucleosides in the Context of NAIL-MS

            Matthias Heiss, Kayla Borland, Yasemin Yoluç, and Stefanie Kellner

 

19. A Method to Monitor the Introduction of Post-Transcriptional Modifications in tRNAs with NMR Spectroscopy

            Alexandre Gato, Marjorie Catala, Carine Tisné, and Pierre Barraud

 

Part VI: Approaches to Assess Kinetics, Determinants, and Functions of RNA Modifications

 

20. Effects of mRNA Modifications on Translation: An Overview

            Bijoyita Roy

 

21. Assaying the Molecular Determinants and Kinetics of RNA Pseudouridylation by H/ACA snoRNAs and Stand-Alone Pseudouridine Synthases

            Dominic P. Czekay, Sarah K. Schultz, and Ute Kothe

 

22. Investigating Pseudouridylation Mechanisms by High-Throughput In Vitro RNA Pseudouridylation and Sequencing

            Nicole M. Martinez and Wendy V. Gilbert

 

23. Targeted RNA m⁶A Editing Using Engineered CRISPR-Cas9 Conjugates

            Xiao-Min Liu and Shu-Bing Qian

Blurb

This detailed book describes some of the most recent advances and up-to-date methodologies to detect, quantify, analyze, and elucidate the biological function of different types of RNA modifications. Importantly, the methodologies and tools described herein can be applied to a wide variety of organisms and can be used to address biological and clinical questions. Beginning with a section on bioinformatics tools, the collection continues with sections on detecting RNA modifications using Nanopore direct RNA sequencing, next-generation sequencing approaches, qPCR- and molecular biology-based methods, mass spectrometry- and NMR-based methods, as well as approaches to assess kinetics, determinants, and functions of RNA modifications. Written for the highly successful Methods in Molecular Biology series style, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, RNA Modifications: Methods and Protocols serves as an ideal guide for those working directly in the fields of epitranscriptomics and post-transcriptional gene regulation, as well as for scientists and clinicians interested in bioinformatic tools to study RNA modifications and techniques to dissect their roles in physiology and disease.