RNA Modifications

1. Front Matter

   Pages i-xiv

   PDF

2. Bioinformatic Tools to Study RNA Modifications

   1. Front Matter

      Pages 1-1

      PDF

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

      • Ilaria Manfredonia, Danny Incarnato

      Pages 3-13

   3. An Informatics Pipeline for Profiling and Annotating RNA Modifications

      • Qi Liu, Xiaoqiang Lang, Richard I. Gregory

      Pages 15-27

3. Detecting RNA Modifications Using Nanopore Direct RNA Sequencing

   1. Front Matter

      Pages 29-29

      PDF

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

      • Huanle Liu, Oguzhan Begik, Eva Maria Novoa

      Pages 31-52

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

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

      Pages 53-74

4. Next-Generation Sequencing Approaches to Detect and Capture Modified RNAs

   1. Front Matter

      Pages 75-75

      PDF

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

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

      Pages 77-95

   3. Transcriptome-Wide Detection of Internal N⁷-Methylguanosine

      • Li-Sheng Zhang, Chang Liu, Chuan He

      Pages 97-104

   4. miCLIP-MaPseq Identifies Substrates of Radical SAM RNA-Methylating Enzyme Using Mechanistic Cross-Linking and Mismatch Profiling

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

      Pages 105-122

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

      • Bryan R. Cullen, Kevin Tsai

      Pages 123-134

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

      • Jun Li, Xingyu Wu, Trung Do, Vy Nguyen, Jing Zhao, Pei Qin Ng et al.

      Pages 135-151

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

      • Erwin L. van Dijk, Claude Thermes

      Pages 153-167

5. Assessing RNA Modifications Using qPCR- and Molecular Biology-Based Methods

   1. Front Matter

      Pages 169-169

      PDF

   2. Assessing 2′-O-Methylation of mRNA Using Quantitative PCR

      • Brittany A. Elliott, Christopher L. Holley

      Pages 171-184

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

      • Ane Olazagoitia-Garmendia, Ainara Castellanos-Rubio

      Pages 185-195

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

      • Jenna M. Lentini, Dragony Fu

      Pages 197-216

   5. Analysis of Queuosine tRNA Modification Using APB Northern Blot Assay

      • Cansu Cirzi, Francesca Tuorto

      Pages 217-230

   6. Detecting ADP-Ribosylation in RNA

      • Deeksha Munnur, Ivan Ahel

      Pages 231-243

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.

• Epitranscriptome
• Post-transcriptional RNA modifications
• Messenger RNA
• Post-transcriptional gene regulation
• Next-generation sequencing
• qPCR

• Department of Urology, University of California, San Francisco, San Francisco, USA

  Mary McMahon

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