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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.
List of contents
Pseudogenes: Four Decades of Discovery.- Methods to Identify and Study the Evolution of Pseudogenes using a Phylogenetic Approach.- Computational Methods For Pseudogene Annotation Based on Sequence Homology.- A Methodology to Study pseudogenized lincRNAs.- GENCODE Pseudogenes.- Comprehensive Detection of Pseudogenes Transcribed by Readthrough.- Mathematical modeling of ceRNA-based interactions.- Pseudogenes as Competitive Endogenous RNAs: Target Prediction and Validation.- Pseudogenes as Competitive Endogenous RNAs: Testing miRNA Dependency.- An Overview of the Computational Models Dealing with the Regulatory ceRNA Mechanism and ceRNA Deregulation in Cancer.- Studying the Oncosuppressive Functions of PTENP1 as a ceRNA.- Methods to Study Protein-Binding to Pseudogene Transcript.- Chromatin Regulation at Parental Gene Promoters by Pseudogene Sense lncRNAs.- Pseudogenes: A Novel Source of Trans Acting Antisense RNAs.- Methods to Study Translated Pseudogenes: Recombinant Expression and Complementation, Targeted Proteomics and RNA Profiling.- A Restriction Endonuclease-Based Assay to distinguish NANOGP8 Retrogene from Parental NANOG.- CRISPR/Cas Technologies Applied to Pseudogenes.- Strategies to Study the Functions of Pseudogenes in Mouse Models of Cancer.- Pseudogene Profiling For Cancer Subtype Classification.- Pseudogenes as Biomarkers and Therapeutic Targets in Human Cancers.- Methods for the Detection of Circulating Pseudogenes and their use as Cancer Biomarker.- Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era.
