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Epitranscriptomics

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Narendra Wajapeyee

    1. Department of Pathology, Yale University School of Medicine, New Haven, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Romi Gupta

    1. Yale Cancer Center, Yale University School of Medicine, New Haven, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 1870)

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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. Bisulfite Sequencing of RNA for Transcriptome-Wide Detection of 5-Methylcytosine

    • Lukas Trixl, Dietmar Rieder, Thomas Amort, Alexandra Lusser
    Pages 1-21

  3. Single-Molecule Analysis of RNA Dynamics in Living Cells Using Molecular Beacons

    • Mingming Chen, Shiqi Mao, Xiaotian Wu, Zhao Ma, Yantao Yang, Christopher J. Krueger et al.
    Pages 23-39

  4. Visualization of Xist Long Noncoding RNA with a Fluorescent CRISPR/Cas9 System

    • Urszula WaÅ›ko, Zeming Zheng, Sanchita Bhatnagar
    Pages 41-50

  5. HAMR: High-Throughput Annotation of Modified Ribonucleotides

    • Lee E. Vandivier, Zachary D. Anderson, Brian D. Gregory
    Pages 51-67

  6. High-Resolution Mapping of N 6-Methyladenosine Using m6A Crosslinking Immunoprecipitation Sequencing (m6A-CLIP-Seq)

    • Phillip J. Hsu, Chuan He
    Pages 69-79

  7. Direct Chemical Biotinylation of RNA 5′-Ends Using a Diazo Reagent

    • Greggory M. Rice, Razvan Nutiu, Christian M. Gampe
    Pages 81-87

  8. Identification of Methylated Transcripts Using the TRIBE Approach

    • Lina Worpenberg, Tobias Jakobi, Christoph Dieterich, Jean-Yves Roignant
    Pages 89-106

  9. Decoding the Atlas of RNA Modifications from Epitranscriptome Sequencing Data

    • Xiao-Qin Zhang, Jian-Hua Yang
    Pages 107-124

  10. Detection of MicroRNA-Mediated Target mRNA Cleavage and 3′-Uridylation in Human Cells by a SLA-RT-PCR Analysis

    • Jing Lin, Lin Ji
    Pages 125-136

  11. Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline

    • Rui Dong, Xu-Kai Ma, Ling-Ling Chen, Li Yang
    Pages 137-149

  12. Synthesis and Evaluation of Novel Neamine–Nucleoside Conjugates as Potential Antibiotic Targets for Escherichia coli 16S Ribosomal RNA

    • Zhen-Jun Yang, Maria-Grazia Concilio, Vasudevan Ramesh, Li-He Zhang
    Pages 151-163

  13. Electron Microscope Detection of 5-Methylcytosine on DNA and RNA

    • Irene Masiello, Marco Biggiogera
    Pages 165-177

  14. Immuno-Northern Blotting: Detection of Modified RNA Using Gel Separation and Antibodies to Modified Nucleosides

    • Eikan Mishima, Takaaki Abe
    Pages 179-187

  15. LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes

    • Xiaowei Chen, Yajing Hao, Ya Cui, Zhen Fan, Runsheng Chen
    Pages 189-198

  16. Guided Reconstruction of Full-Length Isoforms from Short Reads by CIDANE

    • Sandro Andreotti, Stefan Canzar
    Pages 199-208

  17. Profiling of N6-Methyladenosine in Zika Virus RNA and Host Cellular mRNA

    • Gianluigi Lichinchi, Tariq M. Rana
    Pages 209-218

  18. Detection and Quantification of Pseudouridine in RNA

    • Hironori Adachi, Meemanage D. DeZoysa, Yi-Tao Yu
    Pages 219-235

  19. 5-Methylcytosine Analysis by RNA-BisSeq

    • Yu-Sheng Chen, Hai-Li Ma, Ying Yang, Wei-Yi Lai, Bao-Fa Sun, Yun-Gui Yang
    Pages 237-248

  20. RNA Modification Regulatory Genes in DNA Damage

    • Radoslav Janostiak, Narendra Wajapeyee
    Pages 249-262
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Keywords

About this book

This volume provides readers with the latest technologies to study changes in the epitranscriptome. The protocols described in this book explore both targeted and unbiased high-throughput analysis associated with post-transcriptional RNA modification. The chapters in this book also cover specific topics such as transcriptome-wide detection of 5-methylcytosine; HAMR; iRNA-2OM; genome-wide annotation of circRNAs; immune-northern blotting; and detection and quantification of pseudouridine in RNA. 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.

Authoritative and comprehensive, Epitranscriptomics: Methods and Protocols is an important resource for both expert and novice scientists who are interested in learning more aboutthis field.



Editors and Affiliations

  • Department of Pathology, Yale University School of Medicine, New Haven, USA

    Narendra Wajapeyee

  • Yale Cancer Center, Yale University School of Medicine, New Haven, USA

    Romi Gupta

Bibliographic Information

  • Book Title: Epitranscriptomics

  • Book Subtitle: Methods and Protocols

  • Editors: Narendra Wajapeyee, Romi Gupta

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-8808-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-8807-5Published: 12 December 2018

  • eBook ISBN: 978-1-4939-8808-2Published: 11 December 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 298

  • Number of Illustrations: 16 b/w illustrations, 41 illustrations in colour

  • Topics: Human Genetics

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