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The Eukaryotic RNA Exosome

Methods and Protocols

  • Book
  • © 2020

Overview

Editors:
  1. John LaCava

    1. Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA

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  2. Štěpánka Vaňáčová

    1. Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic

    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 2062)

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Table of contents (26 protocols)

  1. Front Matter

    Pages i-xiii
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  2. Introduction to the RNA Exosome in Biomedicine

    1. Front Matter

      Pages 1-1
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    2. The RNA Exosome and Human Disease

      • Milo B. Fasken, Derrick J. Morton, Emily G. Kuiper, Stephanie K. Jones, Sara W. Leung, Anita H. Corbett
      Pages 3-33

  3. Prokaryotic RNases and Exosomes

    1. Front Matter

      Pages 35-35
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    2. The Bacterial Counterparts of the Eukaryotic Exosome: An Evolutionary Perspective

      • Sandra C. Viegas, Rute G. Matos, Cecília M. Arraiano
      Pages 37-46

    3. In Vitro Characterization of the Prokaryotic Counterparts of the Exosome Complex

      • Rute G. Matos, Sandra C. Viegas, Cecília M. Arraiano
      Pages 47-61

    4. Enzymatic Analysis of Reconstituted Archaeal Exosomes

      • Elena Evguenieva-Hackenberg, A. Susann Gauernack, Linlin Hou, Gabriele Klug
      Pages 63-79

  4. Analyzing Exosome Substrates

    1. Front Matter

      Pages 81-81
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    2. Protocols for Northern Analysis of Exosome Substrates and Other Noncoding RNAs

      • Cristina Cruz, Jonathan Houseley
      Pages 83-103Open Access

    3. Mapping Exosome–Substrate Interactions In Vivo by UV Cross-Linking

      • Clémentine Delan-Forino, David Tollervey
      Pages 105-126Open Access

    4. Global Identification of Human Exosome Substrates Using RNA Interference and RNA Sequencing

      • Marta Lloret-Llinares, Torben Heick Jensen
      Pages 127-145

    5. High-Resolution Mapping of 3’ Extremities of RNA Exosome Substrates by 3’ RACE-Seq

      • Hélène Scheer, Caroline De Almeida, Natalia Sikorska, Sandrine Koechler, Dominique Gagliardi, Hélène Zuber
      Pages 147-167

    6. Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion

      • Veronika A. Herzog, Nina Fasching, Stefan L. Ameres
      Pages 169-189

    7. Thiouridine-to-Cytidine Conversion Sequencing (TUC-Seq) to Measure mRNA Transcription and Degradation Rates

      • Alexandra Lusser, Catherina Gasser, Lukas Trixl, Paolo Piatti, Isabel Delazer, Dietmar Rieder et al.
      Pages 191-211

  5. Exosomes and Their Supramolecular Functional Interactions

    1. Front Matter

      Pages 213-213
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    2. RNA Exosomes and Their Cofactors

      • Cornelia Kilchert
      Pages 215-235

    3. Purification of Endogenous Tagged TRAMP4/5 and Exosome Complexes from Yeast and In Vitro Polyadenylation-Exosome Activation Assays

      • Dagmar Zigáčková, Veronika Rájecká, Štěpánka Vaňáčová
      Pages 237-253

    4. Comparative Poly(A)+ RNA Interactome Capture of RNA Surveillance Mutants

      • Cornelia Kilchert, Svenja Hester, Alfredo Castello, Shabaz Mohammed, Lidia Vasiljeva
      Pages 255-276

    5. Purification and In Vitro Analysis of the Exosome Cofactors Nrd1-Nab3 and Trf4-Air2

      • Odil Porrua
      Pages 277-289

    6. Affinity Proteomic Analysis of the Human Exosome and Its Cofactor Complexes

      • Kinga Winczura, Michal Domanski, John LaCava
      Pages 291-325
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Keywords

About this book

This volume provides a cross-section of RNA exosome research protocols, applied to a diversity of model organisms. Chapters guide readers through methods that e.g. delineate eukaryotic exosomes’ origins in prokaryotes, probe its RNA substrates, adapter complexes and macromolecular interaction of networks, and establish critical structural-function relationships. 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 cutting-edge, The Eukaryotic RNA Exosome: Methods and Protocols aims to ensure successful results in the further study of this vital field.


Editors and Affiliations

  • Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA

    John LaCava

  • Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic

    Štěpánka Vaňáčová

About the editors

 

Bibliographic Information

  • Book Title: The Eukaryotic RNA Exosome

  • Book Subtitle: Methods and Protocols

  • Editors: John LaCava, Štěpánka Vaňáčová

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9822-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2020

  • Hardcover ISBN: 978-1-4939-9821-0Published: 26 November 2019

  • Softcover ISBN: 978-1-4939-9824-1Published: 26 November 2020

  • eBook ISBN: 978-1-4939-9822-7Published: 25 November 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 517

  • Number of Illustrations: 27 b/w illustrations, 52 illustrations in colour

  • Topics: Human Genetics, Cell Biology

  • Industry Sectors: Biotechnology, Pharma

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