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RNA Methylation

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Alexandra Lusser

    1. Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1562)

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About this book

This volume provides a comprehensive collection of current methods and protocols to study posttranscriptional base modifications in RNA with special focus on methylation. The protocols in this book discuss state-of-the-art methods for investigating aspects of RNA methylation on different types of RNA. The protocols cover topics such as wet-lab techniques for the detection of methylation, instructions for bioinformatics analyses of transcriptome-scale data, and protocols for the functional examination of RNA modifications and enzymes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions 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.

Cutting-edge and thorough, RNA Methylation: Methods and Protocols is a valuable resource for biochemists and molecular biologists, from various fields, who wish to investigate different types of RNA methylations.

 

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Modifications in Abundant RNA Species

    1. Front Matter

      Pages 1-1
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    2. LC-MS Analysis of Methylated RNA

      • Kathrin Thüring, Katharina Schmid, Patrick Keller, Mark Helm
      Pages 3-18

    3. Comparative Analysis of Ribonucleic Acid Digests (CARD) by Mass Spectrometry

      • Mellie June Paulines, Patrick A. Limbach
      Pages 19-32

    4. Liquid Chromatography-Mass Spectrometry for Analysis of RNA Adenosine Methylation

      • Bi-Feng Yuan
      Pages 33-42

  3. Analysis of N6-Methyladenosine

    1. Front Matter

      Pages 43-43
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    2. Genome-Wide Location Analyses of N6-Methyladenosine Modifications (m6A-Seq)

      • Benoit Molinie, Cosmas C. Giallourakis
      Pages 45-53

    3. Mapping m6A at Individual-Nucleotide Resolution Using Crosslinking and Immunoprecipitation (miCLIP)

      • Anya V. Grozhik, Bastian Linder, Anthony O. Olarerin-George, Samie R. Jaffrey
      Pages 55-78

    4. Detection and Quantification of N 6-Methyladenosine in Messenger RNA by TLC

      • Zsuzsanna Bodi, Rupert G. Fray
      Pages 79-87

  4. Analysis of 5-Methylcytosine

    1. Front Matter

      Pages 89-89
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    2. Illustrating the Epitranscriptome at Nucleotide Resolution Using Methylation-iCLIP (miCLIP)

      • Harry George, Jernej Ule, Shobbir Hussain
      Pages 91-106

    3. Detection of 5-Methylcytosine in Specific Poly(A) RNAs by Bisulfite Sequencing

      • Thomas Amort, Alexandra Lusser
      Pages 107-121

    4. Transcriptome-Wide Detection of 5-Methylcytosine by Bisulfite Sequencing

      • Thomas Amort, Xueguang Sun, Daria Khokhlova-Cubberley, Alexandra Lusser
      Pages 123-142

    5. Analysis of High-Throughput RNA Bisulfite Sequencing Data

      • Dietmar Rieder, Francesca Finotello
      Pages 143-154

    6. Statistical Methods for Transcriptome-Wide Analysis of RNA Methylation by Bisulfite Sequencing

      • Brian J. Parker
      Pages 155-167

  5. Further RNA Modifications

    1. Front Matter

      Pages 169-169
      Download chapter PDF

    2. High-Throughput Mapping of 2′-O-Me Residues in RNA Using Next-Generation Sequencing (Illumina RiboMethSeq Protocol)

      • Virginie Marchand, Lilia Ayadi, Aseel El Hajj, Florence Blanloeil-Oillo, Mark Helm, Yuri Motorin
      Pages 171-187

    3. RiboMeth-seq: Profiling of 2′-O-Me in RNA

      • Nicolai Krogh, Ulf Birkedal, Henrik Nielsen
      Pages 189-209

    4. In Silico Identification of RNA Modifications from High-Throughput Sequencing Data Using HAMR

      • Pavel P. Kuksa, Yuk Yee Leung, Lee E. Vandivier, Zachary Anderson, Brian D. Gregory, Li-San Wang
      Pages 211-229

    5. High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq)

      • Eva Hrabeta-Robinson, Erin Marcus, Aaron E. Cozen, Eric M. Phizicky, Todd M. Lowe
      Pages 231-243
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Editors and Affiliations

  • Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria

    Alexandra Lusser

Bibliographic Information

  • Book Title: RNA Methylation

  • Book Subtitle: Methods and Protocols

  • Editors: Alexandra Lusser

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-6807-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2017

  • Hardcover ISBN: 978-1-4939-6805-3Published: 28 March 2017

  • Softcover ISBN: 978-1-4939-8304-9Published: 20 July 2018

  • eBook ISBN: 978-1-4939-6807-7Published: 27 March 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 304

  • Number of Illustrations: 28 b/w illustrations, 34 illustrations in colour

  • Topics: Human Genetics

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