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Circular RNAs

  • Book
  • © 2024
  • Latest edition

Overview

Editors:
  1. Christoph Dieterich

    1. Klaus Tschira Institute for Integrative Computational Cardiology, University Heidelberg, Heidelberg, Germany

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  2. Marie-Laure Baudet

    1. Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy

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    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 2765)

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About this book

This second edition details new and updated methods on circular RNA. Chapter guide readers through circular RNA purification, in silico characterization, circRNA detection, sequence validation, quantification , techniques related to  gain- and loss-of-function approaches, circular RNA synthesis, split ligation, engineering, nanoparticle packaging, RNA modifications on circular RNA biogenesis, RNA translation potential, and vaccines based on circular RNAs. 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 key tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and cutting-edge, Circular RNAs, Second Edition aims to ensure successful results in the further study of this vital field.

Keywords

Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
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  2. circRNA Purification

    1. Front Matter

      Pages 1-1
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    2. Purification of Circular RNAs Using Poly(A) Tailing Followed by RNase R Digestion

      • Mei-Sheng Xiao, Jeremy E. Wilusz
      Pages 3-19

  3. In Silico circRNA Profiling

    1. Front Matter

      Pages 21-21
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    2. State-of-the-Art Circular RNA Analytics Using the Circtools Software Suite

      • Tobias Jakobi
      Pages 23-46

    3. Exploring Circular RNA Profile and Expression in Extracellular Vesicles

      • Jingjing Zhao, Qiaojuan Li, Shenglin Huang
      Pages 47-59

  4. circRNA Detection, Sequence Validation and Quantification

    1. Front Matter

      Pages 61-61
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    2. In Situ Hybridization of circRNAs in Cells and Tissues through BaseScope™ Strategy

      • Eleonora D’Ambra, Erika Vitiello, Tiziana Santini, Irene Bozzoni
      Pages 63-92

    3. Sanger Sequencing to Determine the Full-Length Sequence of Circular RNAs

      • Suman Singh, Aniruddha Das, Amaresh C. Panda
      Pages 93-105

    4. Droplet Digital PCR for the Detection and Quantification of Bona Fide CircRNAs

      • Linda Masante, Giorgia Susin, Marie-Laure Baudet
      Pages 107-126

    5. Targeted Sequencing of Circular RNAs for Illumina-Based Counting and Nanopore Structure Determination

      • Isabel S. Naarmann-de Vries, Christoph Dieterich
      Pages 127-142

    6. Nanopore-Mediated Sequencing of Circular RNA

      • Morten Trillingsgaard Venø, Junyi Su, Yan Yan, Jørgen Kjems
      Pages 143-157

  5. Functional Study: Tools for Loss- and Gain-of Function Analysis

    1. Front Matter

      Pages 159-159
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    2. In Vivo Tissue-Specific Knockdown of circRNAs Using shRNAs in Drosophila melanogaster

      • Ines Lucia Patop, Michael Canori, Sebastian Kadener
      Pages 161-172

    3. The Functional Circular RNA Screening via RfxCas13d/BSJ-gRNA System

      • Hao Wu, Ling-Ling Chen
      Pages 173-191

    4. Base-Editor-Mediated circRNA Knockout by Targeting Predominantly Back-Splice Sites

      • Xu-Kai Ma, Xiang Gao, Mei Cao, Li Yang
      Pages 193-208

    5. Directed Circularization of a Short RNA

      • Cathrin E. Hansen, Danilo Springstubbe, Sabine Müller, Sonja Petkovic
      Pages 209-226

    6. Engineering Synthetic circRNAs for Efficient CNS Expression

      • Katie N. Clements, Trevor J. Gonzalez, Aravind Asokan
      Pages 227-246

    7. Encapsulating In Vitro Transcribed circRNA into Lipid Nanoparticles Via Microfluidic Mixing

      • Malte Juchem, Sarah Cushman, Dongchao Lu, Shambhabi Chatterjee, Christian Bär, Thomas Thum
      Pages 247-260

  6. Functional Study: Biogenesis and Translation

    1. Front Matter

      Pages 261-261
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Editors and Affiliations

  • Klaus Tschira Institute for Integrative Computational Cardiology, University Heidelberg, Heidelberg, Germany

    Christoph Dieterich

  • Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy

    Marie-Laure Baudet

Bibliographic Information

  • Book Title: Circular RNAs

  • Editors: Christoph Dieterich, Marie-Laure Baudet

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-3678-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024

  • Hardcover ISBN: 978-1-0716-3677-0Published: 22 February 2024

  • Softcover ISBN: 978-1-0716-3680-0Due: 24 March 2024

  • eBook ISBN: 978-1-0716-3678-7Published: 21 February 2024

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XI, 326

  • Number of Illustrations: 5 b/w illustrations, 53 illustrations in colour

  • Topics: Genetics and Genomics

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