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Pseudogenes

Functions and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Laura Poliseno

    1. Oncogenomics Unit, Core Research Laboratory, ISPRO, Institute of Clinical Physiology (IFC), CNR, Pisa, Italy

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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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2324)

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xiii
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  2. Introductory Chapter

    1. Front Matter

      Pages 1-1
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    2. Pseudogenes: Four Decades of Discovery

      • Leonardo Salmena
      Pages 3-18

  3. Methods for Pseudogene Identification

    1. Front Matter

      Pages 19-19
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    2. Methods to Identify and Study the Evolution of Pseudogenes Using a Phylogenetic Approach

      • Jacques Dainat, Pierre Pontarotti
      Pages 21-34

    3. Computational Methods for Pseudogene Annotation Based on Sequence Homology

      • Paul M. Harrison
      Pages 35-48

    4. A Methodology to Study Pseudogenized lincRNAs

      • Sweta Talyan, Miguel A. Andrade-Navarro, Enrique M. Muro
      Pages 49-63

  4. Pseudogene Repositories

    1. Front Matter

      Pages 65-65
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    2. GENCODE Pseudogenes

      • Cristina Sisu
      Pages 67-82

  5. Methods to Study Pseudogene-Related Alterations in Cancer

    1. Front Matter

      Pages 83-83
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    2. Comprehensive Detection of Pseudogenes Transcribed by Readthrough

      • Rui Pinto, Daniel Sobral, Ana Rita Grosso
      Pages 85-102

  6. Methods to Study Transcribed Pseudogenes

    1. Front Matter

      Pages 103-103
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    2. Mathematical Modeling of ceRNA-Based Interactions

      • Andrew Dhawan
      Pages 105-114

    3. Pseudogenes as Competitive Endogenous RNAs: Target Prediction and Validation

      • Florian A. Karreth, Ugo Ala, Paolo Provero, Pier Paolo Pandolfi
      Pages 115-129

    4. Pseudogenes as Competitive Endogenous RNAs: Testing miRNA Dependency

      • Xiaonan Xu, Florian A. Karreth
      Pages 131-147

    5. An Overview of the Computational Models Dealing with the Regulatory ceRNA Mechanism and ceRNA Deregulation in Cancer

      • Federica Conte, Giulia Fiscon, Pasquale Sibilio, Valerio Licursi, Paola Paci
      Pages 149-164

    6. Studying the Oncosuppressive Functions of PTENP1 as a ceRNA

      • Glena Travis, Nahal Haddadi, Ann M. Simpson, Deborah J. Marsh, Eileen M. McGowan, Najah T. Nassif
      Pages 165-185

    7. Methods to Study Protein-Binding to Pseudogene Transcripts

      • Eusebio Chiefari, Biagio Arcidiacono, Maria Mirabelli, Francesco Saverio Brunetti, Emanuela Greco, Daniela Patrizia Foti et al.
      Pages 187-202

    8. Chromatin Regulation at Parental Gene Promoters by Pseudogene Sense lncRNAs

      • Stefan Schoeftner, Michele Scarola, Roberta Benetti
      Pages 203-217

    9. Pseudogenes: A Novel Source of Trans-Acting Antisense RNAs

      • Nicholas C. Lister, Per Johnsson, Paul D. Waters, Kevin V. Morris
      Pages 219-236
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Keywords

About this book

This second edition explores techniques involving pseudogenic DNA, RNA, and proteins. Chapters describe how to identify pseudogenes and how to study the functions and alterations of pseudogenic RNA and proteins, both in vitro, and in vivo. Written in the highly successful Methods in Molecular Biology series format, methodological 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 while avoiding known pitfalls.


Authoritative and cutting-edge, Pseudogenes: Functions and Protocols, Second Edition aims to be a practical guide to researches, useful to help further their study in this field.

Editors and Affiliations

  • Oncogenomics Unit, Core Research Laboratory, ISPRO, Institute of Clinical Physiology (IFC), CNR, Pisa, Italy

    Laura Poliseno

Bibliographic Information

  • Book Title: Pseudogenes

  • Book Subtitle: Functions and Protocols

  • Editors: Laura Poliseno

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1503-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

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

  • Hardcover ISBN: 978-1-0716-1502-7Published: 25 June 2021

  • Softcover ISBN: 978-1-0716-1505-8Published: 26 June 2022

  • eBook ISBN: 978-1-0716-1503-4Published: 24 June 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XIII, 384

  • Number of Illustrations: 78 illustrations in colour

  • Topics: Human Genetics

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