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RNA Modifications

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Mary McMahon

    1. Department of Urology, University of California, San Francisco, San Francisco, USA

    View editor publications

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  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2298)

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About this book

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.

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Table of contents (23 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Bioinformatic Tools to Study RNA Modifications

    1. Front Matter

      Pages 1-1
      Download chapter 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
      Download chapter 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
      Download chapter 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
      Download chapter 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
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Editors and Affiliations

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

    Mary McMahon

Bibliographic Information

  • Book Title: RNA Modifications

  • Book Subtitle: Methods and Protocols

  • Editors: Mary McMahon

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1374-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1373-3Published: 04 June 2021

  • Softcover ISBN: 978-1-0716-1376-4Published: 05 June 2022

  • eBook ISBN: 978-1-0716-1374-0Published: 03 June 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 427

  • Number of Illustrations: 2 b/w illustrations, 72 illustrations in colour

  • Topics: Biochemistry, general

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