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.
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 d N/ d S
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 _29 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
1
Inhaltsverzeichnis
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 F29 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
Klappentext
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.
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
