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Handbook of Epigenetics
The New Molecular and Medical Genetics
3rd Edition - September 8, 2022
Editor: Trygve O Tollefsbol
Hardback ISBN:9780323919098
9 7 8 - 0 - 3 2 3 - 9 1 9 0 9 - 8
eBook ISBN:9780323919500
9 7 8 - 0 - 3 2 3 - 9 1 9 5 0 - 0
Handbook of Epigenetics: The New Molecular and Medical Genetics, Third Edition provides a comprehensive analysis of epigenetics, from basic biology to clinical application. This… Read more
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Handbook of Epigenetics: The New Molecular and Medical Genetics, Third Edition provides a comprehensive analysis of epigenetics, from basic biology to clinical application. This new edition has been fully revised to cover the latest and evolving topics in epigenetics, with chapters updated and new chapters added on topics such as single-cell epigenetics, DNA methylation clocks in age-related diseases, transposable elements and epigenetics, X chromosome inactivation, and the epigenetics of drug addiction, among other topics. Throughout this edition, greater emphasis falls on epigenomic analyses and incorporating multi-omics approaches rather than gene-specific analyses.
In addition, this edition has also been enhanced with step-by-step instructions in research methods, as well as easy-to-digest disease case studies and clinical trials that provide context and applied examples of recent advances in disease understanding and epigenetic therapeutics. These features empower researchers to reproduce the approaches and studies discussed and aid clinical translation. Live links across chapters tie in relevant external datasets and resources.
Provides a timely and comprehensive collection of fully up-to-date coverage of epigenetics
Covers basic epigenetic biology, research methods and technology, disease relationships and clinical medicine
Written at a verbal and technical level that can be understood by scientists and students alike, with chapter summaries and conclusions included throughout
Discusses exciting new topics in epigenetics, such as DNA methylation clocks in age-related diseases, transposable elements and epigenetics, X chromosome inactivation, and the epigenetics of drug addiction
Includes step-by-step instructions in research protocols to aid reproducibility, as well as easy-to-digest disease case studies and clinical trials, providing context and applied examples of recent clinical translation
Researchers working in genetics, biology, molecular biology, pharmaceutical science, and clinical therapy; university researchers, pharmaceutical company and biotechnology researchers interested in drug development and therapies. Advanced undergraduate and graduate students; clinicians
Cover image
Title page
Table of Contents
Copyright
List of contributors
Section I: Overview
Chapter 1. Epigenetics Overview
Abstract
Outline
Introduction
Molecular Mechanisms of Epigenetics
Methods in Epigenetics
Model Organisms of Epigenetics
Factors Influencing Epigenetic Changes
Evolutionary Epigenetics
Epigenetic Epidemiology
Epigenetics and Human Disease
Epigenetic Therapy
The Future of Epigenetics
Conclusion
References
Section II: Molecular Mechanisms of Epigenetics
Chapter 2. Mechanisms of DNA Methylation and Demethylation During Mammalian Development
Abstract
Outline
Introduction
DNA Methylation
DNA Demethylation
Conclusions
Acknowledgments
Glossary
Abbreviations
References
Chapter 3. Mechanisms of Histone Modifications
Abstract
Outline
Introduction
Main Histone Modifications
Role of Aberrant Histone Modifications in Disease
Conclusions
References
Chapter 4. The Epigenetics of Noncoding RNA
Abstract
Outline
Introduction
Conclusions
Acknowledgments
Abbreviations
References
Chapter 5. Prions and prion-like phenomena in epigenetic inheritance
Abstract
Outline
Structural Heredity
Amyloid Prions of Saccharomyces cerevisiae, Podospora anserina, and Other Organisms
Cis Elements Important for Amyloid Prion Formation
Genetic Control of Amyloid Prion Formation and Propagation
Amyloid Prion Variants
Self-Driven Assembly of Hsp60 Mitochondrial Chaperonin
Cytotaxis of Cilia and Other Complex Structures
Mixed Heredity: “Nonamyloid Prions” That Propagate by Auto-activation
Regulatory Inheritance
The Lactose Operon and Its Positive Feedback Loop
Crippled Growth, A Self-sustained and Mitotically Inheritable Signaling Pathway in the Filamentous Fungus Podospora anserina
The White/Opaque Switch of Candida albicans, An Epigenetic Switch at the Transcription Level
Conclusion
References
Chapter 6. Higher-order Chromatin Organization in Diseases, from Chromosomal Position Effect to Phenotype Variegation
Abstract
Outline
Introduction
Chromosomal Position Effect in Human Pathologies
Telomeric Position Effect; Implication in Human Pathologies
Conclusions
References
Chapter 7. Polycomb-group proteins and epigenetic control of gene activity
Abstract
Outline
Introduction
Polycomb Repressive Complexes
Mechanism of Gene Regulation by Polycomb Group Proteins
PcG-Mediated Control of Gene Expression in Stem Cells to Maintain Homeostasis
PcG-mediated Control of Gene Expression in Embryonic Stem Cells
PcG-mediated Control of Gene Expression in Cancer Cells
Conclusion and Future Perspective
Acknowledgment
References
Section III: Methods in Epigenetics
Chapter 8. Methods for Analyzing DNA Cytosine Modifications Genome-wide
Abstract
Outline
Introduction
Methylated DNA Immunoprecipitation
MBD Protein-based Affinity Pulldown
Methylated-CpG Island Recovery Assay
Targeted Bisulfite Sequencing
Infinium and EPIC Methylation Bead Chips
Whole Genome Bisulfite Sequencing
Other Sodium Bisulfite-based Approaches
Enzymatic Methyl-sequencing and Pyrimidine Borane-based Methods
5-Hydroxymethylcytosine Mapping Methodologies
TET-assisted Bisulfite Sequencing
Oxidative Bisulfite Sequencing
APOBEC-coupled Epigenetic Sequencing
SMRT-seq and Nanopore Sequencing
Single Cell Whole Genome Methylation Analysis
Future Directions and Challenges
Acknowledgments
References
Chapter 9. Genome-wide Analyses of Histone Modifications in the Mammalian Genome
Abstract
Outline
Introduction
Histone Modifications in Regulatory Regions
High-throughput Assays for Mapping Histone Modifications
Genome-wide Mapping of Histone Modifications
Catalog of Histone Modification Profiles
Variation of Histone Modifications
Conclusions and Perspectives
ChIP-seq Data Analysis Workflow
Acknowledgments
References
Chapter 10. Techniques for Analyzing Genome-wide Expression of Non-coding RNA
Abstract
Outline
Introduction
cDNA Library Construction
Analysis of RNA-seq Data for ncRNAs
Estimating the Transcription and Degradation Rates of Non-Coding Transcripts
Conclusions
Dyrec-seq Protocol
Acknowledgments
Glossary
References
Chapter 11. Computational Epigenetics: The Competitive Endogenous RNAs Network Analysis
Abstract
Outline
Introduction
Basic Principles of Competitive Endogenous RNAs
The Competitive Endogenous RNAs Network
Mathematical Models for Competitive Endogenous RNAs Network Analysis
Comparison of Mathematical Models for Competitive Endogenous RNAs Network Analysis
Computational Epigenetic Approaches for Competitive Endogenous RNAs Network Analysis
Conclusion
Acknowledgments
References
Section IV: Model Organisms of Epigenetics
Chapter 12. Epigenetic Mechanisms in Bacteria Bridge Physiology, Growth and Host–Pathogen Interactions
Abstract
Outline
Introduction
Protein Phosphorylation in Prokaryotes
DNA Methylation in Bacteria
Protein Methylation
Crosstalks Between Epigenetic Modifications
Conclusions and Future Perspectives
Summary
Protocols for Molecular Modeling
References
Further Reading
Chapter 13. Drosophila Epigenetics
Abstract
Outline
Introduction: Drosophila as a Model Organism in Epigenetic Research
Epigenetic Modification of Histone Proteins Regulate Chromatin Packaging and Gene Control in Drosophila
Position-Effect Variegation
The Role of Epigenetics During Drosophila Development: Epigenetic Memory
Dosage Compensation
The Epigenetic Language in Postmitotic Neurons Underlying Cognitive Function
Conclusion
Protocol
Glossary
Abbreviations
References
Chapter 14. Models of Mouse Epigenetic Inheritance: Classification, Mechanisms, and Experimental Strategies
Abstract
Outline
Introduction
Epigenetic Programming in Gametogenesis
Epigenetic Re-Programming During Embryogenesis
Metastable Epialleles
Genomic Imprinting
Conclusions
Acknowledgments
References
Chapter 15. Plant Epigenomics
Abstract
Outline
Introduction
Basic Mechanisms of Plant Epigenome Regulation
Epigenetic Phenomena in Plants
Epigenetic Regulation of Transposable Elements and Interactions With Genes
Epigenetic Regulation of Stress Responses in Plants
Emerging Technologies for Epigenome Studies in Plants
Future Perspectives
References
Section V: Factors Influencing Epigenetic Changes
Chapter 16. Dynamic Changes in Epigenetic Modifications During Mammalian Early Embryo Development
Abstract
Outline
Introduction
DNA methylation during mammalian early embryo development
Dynamic changes and function of histone modifications in early embryo development
Summary
References
Chapter 17. Epigenetic Biomarkers
Abstract
Outline
Introduction
Epigenetic biomarkers offer distinct advantages over genetic biomarkers
Minimally invasive tissues are suitable for detecting epigenetic biomarkers
Field cancerization and epigenetic biomarkers
Potential DNA methylation biomarkers in cancer and other diseases
Potential m6A methylation biomarkers in cancer and other diseases
Potential histone modification biomarkers in cancer and other diseases
Potential non-coding RNA biomarkers in diseases
Epigenetic biomarker detection methods in the clinic
Challenges and future perspectives
Abbreviations
References
Chapter 18. Transposable Elements Shaping the Epigenome
Abstract
Outline
Introduction
Classification and structure of transposable elements
Transposable elements genomic annotation
Epigenetic control of transposable elements
Factors influencing transposable elements epigenetics
Influence of transposable elements on host epigenetics
Concluding remarks
References
Chapter 19. Dietary and Metabolic Compounds Affecting Covalent Histone Modifications
Abstract
Outline
Introduction
Metabolic and Dietary Control of Histone and Transcriptional Dynamics
Regulation of Chromatin Dynamics
Histone Demethylation
Histone Acetylation
Other Histone Modifications
Concluding Perspectives
Acknowledgments
Abbreviations
References
Further reading
Chapter 20. Epigenetics, Stem Cells, Cellular Differentiation, and Associated Neurological Disorders and Brain Cancer
Abstract
Outline
Introduction to Epigenetics
Epigenetics and the Human Brain
Epigenetics and Glioblastoma
Epigenetic Changes in Glioma Stem Cells
Genes Involved in Glioblastoma
Stem Cell Transplantations in Glioblastoma
Neural Stem Cell Transplantation for GB
Conclusions
Abbreviations
References
Chapter 21. Epigenetic Regulation of Skeletal Muscle Regeneration
Abstract
Outline
Introduction
Epigenetic Control in the Maintenance of Quiescence
Epigenetic Control of the Activation and Proliferation of SCs
Epigenetic Control of SCs Differentiation
Small Molecules as a Therapeutic Alternative in the Epigenetic Control of Regeneration
Conclusion
Acknowledgments
References
Chapter 22. Epigenetics of X-chromosome Inactivation
Abstract
Outline
Introduction
Brief Historical Perspective of XCI
X-chromosome Evolution and the Incomplete Nature of XCI
Imprinted and Random XCI
XCI Regulation and Main Epigenetic Steps
XCI Differences Between Mice and Humans
X-autosome Dosage Compensation
Methods for Exploring XCI Status
Physiological and Pathogenic XCI Skewing
X-chromosome, Sex Bias and Diseases
XCI Plasticity: Opportunities for Epigenetic Therapeutics
Use of Epigenetic Modifications as Potential Biomarkers
Use of Epigenetic Modifiers for Potential Diagnosis and Therapy in Autoimmune Diseases
Summary
Multiomics and machine learning accurately predict clinical response to adalimumab and etanercept therapy in patients with rheumatoid arthritis [ex: Autoimmunity Epigenetics Case Study]
Abbreviations
References
Chapter 37. Epigenetics of Brain Disorders
Abstract
Outline
Introduction
Important Epigenetic Mechanisms for the Brain
Epigenetic Dysregulation in Neurodevelopmental Disorders: The Example of Rett Syndrome
Epigenetic Dysregulation in Neurodegenerative Disorders: The Example of Alzheimer’s Disease
Epigenetic Dysregulation in Psychiatric Disorders: The Example of Depression
Epigenetic Dysregulation by Environmental Stress: The Example of Early-life Stress
Conclusions and Outlook
Summary
Research case study
Acknowledgments
References
Chapter 38. Epigenetics of Metabolic Diseases
Abstract
Outline
Introduction
Impact of Age and Lifestyle Factors on the Epigenome
Epigenetic Memory, Prenatal Exposure, and Risk of Metabolic Disease
Epigenetic Features of Metabolic Diseases
Conclusions
Abbreviations
References
Chapter 39. Imprinting Disorders in Humans
Abstract
Outline
Introduction
Clinical Findings in Imprinting Disorders
Molecular Findings in Imprinting Disorders
Causes of Disturbed Imprinting
Cis-acting Factors
Trans-acting Factors
Maternal Effect Mutations and Multilocus Imprinting Disturbance
Translational Use of New Findings in ImpDis and New Methodologies
Genetic and Reproductive Counseling
Clinical Management
Concluding Remarks
References
Section IX: Epigenetic Therapy
Chapter 40. Clinical Applications of Histone Deacetylase Inhibitors
Abstract
Outline
Introduction
HDACi for the Treatment of Hematological Malignancies
HDACi in the Treatment of Solid Tumors
Clinical Applications of HDACi for Noncancer Diseases
Conclusions and the Future Directions of the Clinical Applications of HDACi
References
Chapter 41. Combination Epigenetic Therapy
Abstract
Outline
Introduction
Chromatin-remodeling Agents, Combined Treatment, and Targeted Therapy
DNA Methylation/Demethylation and Combined Treatment
Histone Modifications and Histone-modifying Enzymes for Epigenetic Treatment
Conclusions and Future Perspectives
Clinical Trial
References
Section X: The Future of Epigenetics
Chapter 42. New Directions for Epigenetics: Application of Engineered DNA-binding Molecules to Locus-specific Epigenetic Research
Abstract
Outline
Introduction
General Information on Engineered DNA-binding Molecules
Locus-specific Epigenome Editing
Locus-specific Identification of Epigenetic Molecules that Interact with Target Genomic Regions
Conclusions
References
Index
No. of pages: 918
Language: English
Published: September 8, 2022
Imprint: Academic Press
Hardback ISBN: 9780323919098
eBook ISBN: 9780323919500
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Trygve O Tollefsbol
Dr. Tollefsbol is a Distinguished Professor of Biology and a Senior Scientist in the O’Neal Comprehensive Cancer Center, Integrative Center for Aging Research, Nutrition Obesity Research Center, University Wide Microbiome Center, and the Comprehensive Diabetes Center at the University of Alabama at Birmingham (UAB). He is Director of the UAB Cell Senescence Culture Facility which he established in 1999. Dr. Tollefsbol trained as a Postdoctoral Fellow and Assistant Research Professor with members of the National Academy of Science at Duke University and the University of North Carolina. He earned doctorates in molecular biology and osteopathic medicine from the University of North Texas Health Sciences Center and his bachelor’s degree in Biology from the University of Houston. He has received prior funding from the NCI, NHLBI, NIMH and other federal institutes as well as the Glenn Foundation for Medical Research, Susan G. Komen for the Cure, the American Federation for Aging Research (AFAR), and the American Institute for Cancer Research (AICR) among many other sources.
Affiliations and expertise
Distinguished Professor of Biology, University of Alabama at Birmingham, AL, USA