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Biomedical Sciences - Human Genetics | Pseudogenes - Functions and Protocols


Functions and Protocols

Series: Methods in Molecular Biology, Vol. 1167

Poliseno, Laura (Ed.)

2014, X, 319 p. 58 illus., 38 illus. in color.

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  • Includes cutting-edge methods and protocols for the study of pseudogenes and the avoidance of inadvertent detection
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Providing a list of methods useful both to those who wish to study pseudogenes and to those who actually want to avoid their inadvertent detection, Pseudogenes: Functions and Protocols explores techniques involving pseudogenic DNA, RNA, and peptides/proteins, once believed to lack any functionality, but now known to be involved in complex regulatory circuits. After a few introductory chapters that overview the functions so far attributed to pseudogenes, this thorough volume delves into methods for pseudogene identification, for the detection of pseudogene transcription and translation, and for the study of the functions of pseudogenic RNA and proteins, as well as methods to avoid pseudogene detection when the focus of the research is their highly homologous parental counterparts.  As part of the highly successful Methods in Molecular Biology series, chapters feature the kind of detailed descriptions and implementation advice that ensures successful results in the lab.


Authoritative and practical, Pseudogenes: Functions and Protocols will contribute to the high interest of the scientific community toward pseudogenes, while stimulating the conception of pseudogene-centered research projects and providing experimental protocols that can facilitate their execution.

Content Level » Professional/practitioner

Keywords » Inadvertent detection - Non-coding genome - Pseudogene identification - Pseudogenic DNA and RNA - Pseudogenic proteins - Regulatory long non-coding RNAs - Transcribed pseudogenes

Related subjects » Human Genetics

Table of contents 

Part I: Introductory Chapters


1. Pseudogene Redux with New Biological Significance

            Leonardo Salmena


2. Contribution of Pseudogenes to Sequence Diversity

            Mauno Vihinen


Part II: Methods to Identify Pseudogenes


3. Computational Methods for Pseudogene Annotation Based on Sequence Homology

            Paul M. Harrison


4. Computational Methods of Identification of Pseudogenes Based on Functionality: Entropy and GC Content

            Evgeniy S. Balakirev, Vladimir R. Chechetkin, Vasily V. Lobzin, and Francisco J. Ayala


5. Computational Methods of Identification of Pseudogenes Based on Functionality: Hybridization of 18S rRNA and mRNA During Translation

            Chuanhua Xing


6. Whole Genome Identification of Neutrally Evolving Pseudogenes Using the Evolutionary Measure dN/dS

            Lisa O. Andrieux and David Torrents Arenales


7. Methods to Study the Occurrence and the Evolution of Pseudogenes Through a Phylogenetic Approach

            Jacques Dainat and Pierre Pontarotti


Part III: Methods to Detect Transcribed Pseudogenes of a Parental Gene of Interest


8. Methods for Detecting Transcribed Pseudogenes: PCR on Regions of High Sequence Similarity Followed by Cloning and Sequencing

            Wenyong Ding and Jianwu Dai


Part IV: High-Throughput Methods to Detect Transcribed Pseudogenes


9. RNA Amplification for Pseudogene Detection Using RNA-Seq

            Stephen C.M. Tsoi and Michael K. Dyck


10. GENCODE Pseudogenes

            Adam Frankish and Jennifer Harrow


11. Methods to Detect Transcribed Pseudogenes: RNA-Seq Discovery Allows Learning Through Features

            Camilo Valdes and Enrico Capobianco


Part V: High-Throughput Methods to Detect Translated Pseudogenes


12. Proteomics Techniques for the Detection of Translated Pseudogenes

            Nadia Ucciferri and Silvia Rocchiccioli


Part VI: Methods to Study Transcribed Pseudogenes


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

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


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

            Per Johnsson, Kevin V. Morris, and Dan Grandér


15. Pseudogene-Derived Endogenous siRNAs and Their Function

            Wen-Ling Chan and Jan-Gowth Chang


Part VII: Methods to Study Translated Pseudogenes


16. Methods to Study Translated Pseudogenes: In Vitro Translation, Fusion with a Tag/Reporter Gene, and Complementation Assay

            Anne Parle-McDermott


Part VIII: Methods to Study Translated Pseudogenes


17. Targeted and Robust Amplification of Mitochondrial DNA in the Presence of Nuclear Encoded Mitochondrial Pseudogenes Using Φ29 DNA Polymerases

            Jonci N. Wolff


18. Discrimination of Pseudogene and Parental Gene DNA Methylation Using Allelic Bisulphite Sequencing

            Luke B. Hesson and Robyn L. Ward


19. Mutational Analysis of CYP21A2 Gene and CYP21A1P Pseudogene: Long Range PCR on Genomic DNA

            Hsien-Hsiung Lee


20. PMS2 Gene Mutational Analysis: RNA-Based Direct cDNA Sequencing to Circumvent Pseudogene Interference

            Katharina Wimmer and Annekatrin Wernstedt


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

Kathleen Claes and Kim De Leeneer

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