Main description:

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.

Contents:

Part I: Introductory Chapter

1. Pseudogenes: Four Decades of Discovery

Leonardo Salmena

Part II: Methods for Pseudogene Identification

2. Methods to Identify and Study the Evolution of Pseudogenes using a Phylogenetic Approach

Jacques Dainat and Pierre Pontarotti

3. Computational Methods For Pseudogene Annotation Based on Sequence Homology

Paul M. Harrison

4. A Methodology to Study pseudogenized lincRNAs

Sweta Talyan, Miguel A. Andrade-Navarro, and Enrique M. Muro

Part III: Pseudogene Repositories

5. GENCODE Pseudogenes

Cristina Sisu

Part IV: Methods to Study Pseudogene-Related Alterations in Cancer

6. Comprehensive Detection of Pseudogenes Transcribed by Readthrough

Rui Pinto, Daniel Sobral, and Ana Rita Grosso

Part V: Methods to Study Transcribed Pseudogenes

7. Mathematical modeling of ceRNA-based interactions

Andrew Dhawan

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

Florian A. Karreth, Ugo Ala, Paolo Provero, and Pier Paolo Pandolfi

9-Pseudogenes as Competitive Endogenous RNAs: Testing miRNA Dependency

Xiaonan Xu and Florian A. Karreth

10. 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, and Paola Paci

11. Studying the Oncosuppressive Functions of PTENP1 as a ceRNA

Glena Travis, Nahal Haddadi, Ann M. Simpson, Deborah J. Marsh, Eileen M. McGowan, and Najah T. Nassif

12. Methods to Study Protein-Binding to Pseudogene Transcripts

Eusebio Chiefari, Biagio Arcidiacono, Maria Mirabelli, Francesco Saverio Brunetti, Domenica Maria Corigliano, Daniela Patrizia Foti, and Antonio Brunetti

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

Stefan Schoeftner, Michele Scarola, and Roberta Benetti

14.Pseudogenes: A Novel Source of Trans Acting Antisense RNAs

Nicholas C. Lister, Per Johnsson, Paul D. Waters, and Kevin V. Morris

Part VI: Methods to Study Translated Pseudogenes

15. Methods to Study Translated Pseudogenes: Recombinant Expression and Complementation, Targeted Proteomics and RNA Profiling

Anne Parle-McDermott, Niamh Bookey, Paula Meleady and Paola Drago

16. A Restriction Endonuclease-Based Assay to distinguish NANOGP8 Retrogene from Parental NANOG

Hamida Thakur and Abid R. Mattoo

Part VII: CRISPR/CAS9 Technology Applied To Pseudogenes

17-CRISPR/Cas Technologies Applied to Pseudogenes

Marianna Vitiello and Laura Poliseno

Part VIII: In Vivo Models to Study Pseudogenes

18. Strategies to Study the Functions of Pseudogenes in Mouse Models of Cancer

Ilah Bok and Florian A. Karreth

Part IX: Clinical Relevance of Pseudogenes

19. Pseudogene Profiling For Cancer Subtype Classification

Yan Zhang and Deyou Zheng

20. Pseudogenes as Biomarkers and Therapeutic Targets in Human Cancers

Cristina Sisu

21. Methods for the Detection of Circulating Pseudogenes and their use as Cancer Biomarkers

Manjusha Vaidya and Kiminobu Sugaya

Part X: Methods To Avoid Pseudogene Detection

22. Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era

Kathleen B.M. Claes, Toon Rosseel, and Kim De Leeneer