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HANDBOOK OF EPIGENETICS
 HANDBOOK OF
EPIGENETICS
The New Molecular and Medical
Genetics
THIRD EDITION

Edited by

TRYGVE O. TOLLEFSBOL
Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States; O’Neal Comprehensive Cancer Center,
University of Alabama at Birmingham, Birmingham, AL, United States; Integrative Center for Aging Research, University of Alabama at
Birmingham, Birmingham, AL, United States; Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL,
United States; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States; University Wide
Microbiome Center, University of Alabama at Birmingham, Birmingham, AL, United States
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 Contents

List of contributors xiii 4. The Epigenetics of Noncoding RNA 55

RAVINDRESH CHHABRA

I Introduction 55
Overview Conclusions 67
Acknowledgments 67
References 68
1. Epigenetics Overview 3
TRYGVE O. TOLLEFSBOL 5. Prions and prion-like phenomena in
epigenetic inheritance 73
Introduction 3 PHILIPPE SILAR
Molecular Mechanisms of Epigenetics 3
Methods in Epigenetics 4 Structural Heredity 74
Model Organisms of Epigenetics 5 Amyloid Prions of Saccharomyces cerevisiae,
Factors Influencing Epigenetic Changes 5 Podospora anserina, and Other Organisms 74
Evolutionary Epigenetics 6 Cis Elements Important for Amyloid Prion Formation 76
Epigenetic Epidemiology 6 Genetic Control of Amyloid Prion Formation and
Epigenetics and Human Disease 7 Propagation 76
Epigenetic Therapy 7 Amyloid Prion Variants 77
The Future of Epigenetics 7 Self-Driven Assembly of Hsp60 Mitochondrial Chaperonin 77
Conclusion 8 Cytotaxis of Cilia and Other Complex Structures 78
References 8 Mixed Heredity: “Nonamyloid Prions” That Propagate by
Auto-activation 78
II Regulatory Inheritance
The Lactose Operon and Its Positive Feedback Loop
79
79
Molecular Mechanisms of Epigenetics Crippled Growth, A Self-sustained and Mitotically
Inheritable Signaling Pathway in the Filamentous Fungus
Podospora anserina 80
The White/Opaque Switch of Candida albicans,
2. Mechanisms of DNA Methylation and
An Epigenetic Switch at the Transcription Level 81
Demethylation During Mammalian Conclusion 82
Development 11 References 83
ZHENGZHOU YING AND TAIPING CHEN

Introduction 11 6. Higher-order Chromatin Organization in

DNA Methylation 12 Diseases, from Chromosomal Position Effect to
DNA Demethylation 17 Phenotype Variegation 89
Conclusions 20 FRÉDÉRIQUE MAGDINIER AND JÉRÔME D. ROBIN
Acknowledgments 21
References 22 Introduction 89
Chromosomal Position Effect in Human Pathologies 93
Telomeric Position Effect; Implication in Human Pathologies 98
3. Mechanisms of Histone Modifications 27 Conclusions 101
LUDOVICA VANZAN, ATHENA SKLIAS, MARIA BOSKOVIC, References 102
ZDENKO HERCEG, RABIH MURR AND DAVID M. SUTER

Introduction 27 7. Polycomb-group proteins and epigenetic

Main Histone Modifications 28 control of gene activity 111
Role of Aberrant Histone Modifications in Disease 45 PRASAD PETHE
Conclusions 45
References 46 Introduction 111

v
vi Contents

Polycomb Repressive Complexes 112 10. Techniques for Analyzing Genome-wide

Mechanism of Gene Regulation by Polycomb Expression of Non-coding RNA 163
Group Proteins 112
RENA ONOGUCHI-MIZUTANI, KENZUI TANIUE,
PcG-Mediated Control of Gene Expression in KENTARO KAWATA, TOSHIMICHI YAMADA AND
Stem Cells to Maintain Homeostasis 114 NOBUYOSHI AKIMITSU
PcG-mediated Control of Gene Expression in
Embryonic Stem Cells 116 Introduction 163
PcG-mediated Control of Gene Expression in cDNA Library Construction 164
Cancer Cells 117 Analysis of RNA-seq Data for ncRNAs 169
Conclusion and Future Perspective 118 Estimating the Transcription and
Acknowledgment 118 Degradation Rates of Non-Coding Transcripts 172
References 118 Conclusions 174
Dyrec-seq Protocol 175
Acknowledgments 177
III References 178
Methods in Epigenetics
11. Computational Epigenetics:
8. Methods for Analyzing DNA Cytosine The Competitive Endogenous RNAs Network
Modifications Genome-wide 123 Analysis 185
TIBOR A. RAUCH AND GERD P. PFEIFER LOO KEAT WEI

Introduction 123 Introduction 185

Methylated DNA Immunoprecipitation 124 Basic Principles of Competitive Endogenous RNAs 185
MBD Protein-based Affinity Pulldown 124 The Competitive Endogenous RNAs Network 186
Methylated-CpG Island Recovery Assay 125 Mathematical Models for Competitive Endogenous RNAs
Targeted Bisulfite Sequencing 125 Network Analysis 187
Infinium and EPIC Methylation Bead Chips 127 Comparison of Mathematical Models for Competitive
Whole Genome Bisulfite Sequencing 127 Endogenous RNAs Network Analysis 190
Other Sodium Bisulfite-based Approaches 128 Computational Epigenetic Approaches for Competitive
Enzymatic Methyl-sequencing and Pyrimidine Endogenous RNAs Network Analysis 190
Borane-based Methods 129 Conclusion 195
5-Hydroxymethylcytosine Mapping Methodologies 130 Acknowledgments 196
TET-assisted Bisulfite Sequencing 131 Conflict of Interest Statement 196
Oxidative Bisulfite Sequencing 131 References 196
APOBEC-coupled Epigenetic Sequencing 131
SMRT-seq and Nanopore Sequencing 131
Single Cell Whole Genome Methylation Analysis 132
Future Directions and Challenges 133 IV
Acknowledgments 133 Model Organisms of Epigenetics
References 133

9. Genome-wide Analyses of Histone 12. Epigenetic Mechanisms in Bacteria Bridge

Modifications in the Mammalian Genome 137 Physiology, Growth and Host Pathogen
Interactions 201
SHULAN TIAN, SUSAN L. SLAGER, ERIC W. KLEE AND
HUIHUANG YAN MARIA MIAH, MIHALY MEZEI AND SHIRAZ MUJTABA

Introduction 137 Introduction 201

Histone Modifications in Regulatory Regions 138 Protein Phosphorylation in Prokaryotes 201
High-throughput Assays for Mapping Histone DNA Methylation in Bacteria 204
Modifications 139 Protein Methylation 207
Genome-wide Mapping of Histone Modifications 145 Crosstalks Between Epigenetic Modifications 209
Catalog of Histone Modification Profiles 149 Conclusions and Future Perspectives 209
Variation of Histone Modifications 149 Summary 210
Conclusions and Perspectives 153 Protocols for Molecular Modeling 210
ChIP-seq Data Analysis Workflow 154 References 211
Acknowledgments 157 Further Reading 213
References 158
 Contents vii
13. Drosophila Epigenetics 215 DNA methylation during mammalian early embryo
AKANKSHA BHATNAGAR, ASHLEY M. KARNAY AND
development 291
FELICE ELEFANT Dynamic changes and function of histone modifications
in early embryo development 293
Introduction: Drosophila as a Model Organism in Epigenetic Summary 298
Research 216 References 299
Epigenetic Modification of Histone Proteins
Regulate Chromatin Packaging and Gene Control in
Drosophila 217
Position-Effect Variegation 220
17. Epigenetic Biomarkers 303
The Role of Epigenetics During Drosophila Development: XIAOTONG HU
Epigenetic Memory 223
Dosage Compensation 229 Introduction 303
The Epigenetic Language in Postmitotic Neurons Epigenetic biomarkers offer distinct advantages
Underlying Cognitive Function 232 over genetic biomarkers 304
Conclusion 238 Minimally invasive tissues are suitable for detecting
Protocol 238 epigenetic biomarkers 305
References 241 Field cancerization and epigenetic biomarkers 306
Potential DNA methylation biomarkers in cancer and
other diseases 307
14. Models of Mouse Epigenetic Inheritance: Potential m6A methylation biomarkers in cancer and
Classification, Mechanisms, and Experimental other diseases 308
Potential histone modification biomarkers in cancer and
Strategies 249
other diseases 309
COURTNEY W. HANNA Potential non-coding RNA biomarkers in diseases 310
Epigenetic biomarker detection methods in the clinic 313
Introduction 249
Challenges and future perspectives 316
Epigenetic Programming in Gametogenesis 250
References 317
Epigenetic Re-Programming During Embryogenesis 251
Metastable Epialleles 251
Genomic Imprinting 253
Conclusions 259 18. Transposable Elements Shaping the
Acknowledgments 259 Epigenome 323
References 259 KAREN GIMÉNEZ-ORENGA AND ELISA OLTRA

Introduction 323
15. Plant Epigenomics 263 Classification and structure of transposable elements 324
LEONARDO FURCI, JÉRÉMY BERTHELIER, OSCAR JUEZ, MATIN Transposable elements genomic annotation 328
MIRYEGANEH AND HIDETOSHI SAZE Epigenetic control of transposable elements 329
Factors influencing transposable elements epigenetics 334
Introduction 263
Influence of transposable elements on host epigenetics 335
Basic Mechanisms of Plant Epigenome Regulation 264
Concluding remarks 343
Epigenetic Phenomena in Plants 268
References 343
Epigenetic Regulation of Transposable Elements and
Interactions With Genes 269
Epigenetic Regulation of Stress Responses in Plants 271
Emerging Technologies for Epigenome Studies in Plants 276 19. Dietary and Metabolic Compounds
Future Perspectives 278 Affecting Covalent Histone Modifications 357
References 279 GARETH W. DAVISON

Introduction 357
V Metabolic and Dietary Control of Histone and
Transcriptional Dynamics 359
Factors Influencing Epigenetic Changes Regulation of Chromatin Dynamics 360
Histone Demethylation 362
Histone Acetylation 367
16. Dynamic Changes in Epigenetic Modifications Other Histone Modifications 373
During Mammalian Early Embryo Development 289 Concluding Perspectives 374
JIE YANG AND WEI JIANG Acknowledgments 375
References 375
Introduction 289 Further reading 380
viii Contents

20. Epigenetics, Stem Cells, Cellular Histone Acetylation and HATs 445
Differentiation, and Associated Neurological Histone Deacetylation and Histone Deacetylases 447
Histone Methylation 448
Disorders and Brain Cancer 381
Histone Modifications: Gene Expression 449
BHAIRAVI SRINAGESHWAR, GARY L. DUNBAR AND Manipulating Histone Modifications 450
JULIEN ROSSIGNOL
DNA Methylation and Long-term Memory 452
Introduction to Epigenetics 382 Histone Variant Exchange 456
Epigenetics and the Human Brain 383 Epitranscriptomics: RNA Epigenetics 457
Epigenetics and Glioblastoma 394 Summary 458
Epigenetic Changes in Glioma Stem Cells 394 Acknowledgments 458
Genes Involved in Glioblastoma 395 References 458
Stem Cell Transplantations in Glioblastoma 396
Neural Stem Cell Transplantation for GB 397
Conclusions 397
24. Transgenerational Epigenetics 465
References 398 JAMES P. CURLEY, RAHIA MASHOODH AND
FRANCES A. CHAMPAGNE

21. Epigenetic Regulation of Skeletal Muscle Introduction 465

Epigenetic Consequences of Prenatal Maternal Exposures 466
Regeneration 403
Postnatal Maternal Regulation of the Epigenome 468
RODOLFO DANIEL ÁVILA-AVILÉS, CLAUDIA NEGRÓN-LOMAS AND Paternal Influence on Offspring Development 469
J. MANUEL HERNÁNDEZ-HERNÁNDEZ
Transgenerational Effects of Parental Influence 469
Introduction 403 Germline-mediated Transgenerational Inheritance 470
Epigenetic Control in the Maintenance of Quiescence 404 Experience-dependent Epigenetic Inheritance 471
Epigenetic Control of the Activation and Proliferation Epigenetics, Plasticity, and Evolving Concepts of
of SCs 406 Inheritance 472
Epigenetic Control of SCs Differentiation 408 Summary 473
Small Molecules as a Therapeutic Alternative in the Acknowledgments 473
Epigenetic Control of Regeneration 410 References 473
Conclusion 412
Acknowledgments 413
References 413
25. DNA Methylation Clocks in Age-related
Disease 479
PETER D. FRANSQUET, JO WRIGGLESWORTH AND JOANNE RYAN
22. Epigenetics of X-chromosome Inactivation 419
CÍNTIA BARROS SANTOS-REBOUÇAS Aging 479
Epigenetic Clocks 480
Introduction 419 First Generation Epigenetic Clocks 480
Brief Historical Perspective of XCI 420 Second Generation Epigenetic Clocks 484
X-chromosome Evolution and the Incomplete Nature Epigenetic Clocks and Age-related Disease 485
of XCI 420 Epigenetic Clocks Without an Age-related Disease Focus 488
Imprinted and Random XCI 422 Can Epigenetic Age be Modified? 489
XCI Regulation and Main Epigenetic Steps 423 Summary 491
XCI Differences Between Mice and Humans 427 References 491
X-autosome Dosage Compensation 427
Methods for Exploring XCI Status 429
Physiological and Pathogenic XCI Skewing 429 VI
X-chromosome, Sex Bias and Diseases 432 Evolutionary Epigenetics
XCI Plasticity: Opportunities for Epigenetic Therapeutics 434
Concluding Remarks 434
Acknowledgments 434
References 436
26. Evolution of Epigenetic Mechanisms
in Plants: Insights from H3K4 and H3K27
Methyltransferases 499
23. Epigenetics of Memory Processes 443 J. ARMANDO CASAS-MOLLANO, ERICKA ZACARIAS AND
SRAVANI PULYA AND BALARAM GHOSH JULIANA ALMEIDA

Introduction 443 Introduction 499

Histone Posttranslational Modifications: Long-term Memory Histone Lysine Methylation 500
Regulation 444 Histone Lysine Methyltransferases in Plants 500
 Contents ix
Evolution of Plant Histone Lysine Methyltransferases Livestock Epigenetics Case Study 595
Methylating H3K4 502 Acknowledgment 598
Evolution of Plant Histone Lysine Methyltransferases References 599
Methylating H3K27 508
Perspectives 514
Acknowledgments 515 30. Nutritional Epigenetics and Fetal Metabolic
References 515 Programming 611
HO-SUN LEE

27. Evolution, Functions and Dynamics of Introduction 611

Epigenetic Mechanisms in Animals 521 Metabolic Sensing by Epigenetic Mechanisms 612
GÜNTER VOGT Impact of Prenatal Nutrition on Fetal Reprogramming 615
Maternal Diet and Metabolic Epigenome 616
Introduction 521 Summary and Perspectives 619
Evolution of Epigenetic Mechanisms in The Animal Acknowledgments 620
Kingdom 521 References 620
Features of Epigenetic Mechanisms and Role in Gene
Regulation 524
Dynamics of Epigenetic Marks During Development 526 31. Epigenetics of Drug Addiction 625
Generation of Phenotypic Variation in Populations by RYAN D. SHEPARD AND FERESHTEH S. NUGENT
Epigenetic Mechanisms 530
Relevance of Epigenetics for Animal Ecology 534 Introduction 625
Relevance of Epigenetics for Animal Evolution 538 What Is Addiction? 626
Conclusions and Perspectives 543 Dopamine and Reward Circuits 626
Summary 545 Synaptic Plasticity, Learning and Memory and
References 545 Addiction 628
Epigenetic Processes in Drug Addiction 630
Utilizing Epigenetic Targets for Diagnosis and Treatments to
28. Adaptive evolution and epigenetics 551 Combat Addiction and SUDs 632
ILKKA KRONHOLM Conclusion 634
Summary 634
Introduction 551 Acknowledgments 634
Epigenetic Variation 551 References 634
Modeling Evolution 552 Further Reading 637
Induced Epigenetic Changes 552
Spontaneous Epigenetic Variation 554
Modeling Spontaneous Epigenetic Variation 555 32. Environmental Influence on Epigenetics 639
Limits of Epigenetic Contributions to Adaptation 559 MARISOL RESENDIZ, DARRYL S. WATKINS,
Conclusions and Future Directions 560 NAIL CAN ÖZTÜRK AND FENG C. ZHOU
Acknowledgments 561
References 561 Introduction 639
The Extent (Timeline) of Environmental Influence 641
Exerting Environment 642
VII Mental or Physiological Environment 643
Hazardous Environmental Pollutants and Chemicals 650
Epigenetic Epidemiology Conclusion and Future Direction 658
Research case study [18] 660
References 663
29. Epigenetics of Livestock Health, Production,
and Breeding 569
EVELINE M. IBEAGHA-AWEMU AND HASAN KHATIB
33. Gut Microbiome Influence on Human
Epigenetics, Health, and Disease 669
Introduction 569 MARTIN M. WATSON, MARK VAN DER GIEZEN AND KJETIL SØREIDE
Development of Animal Breeding 570
Epigenetic Source of Phenotypic Variation in Livestock Introduction 669
Health and Production 571 Early Microbiome Exposure and Epigenetic Influence 673
Revisiting Animal Breeding Planning and Management: Human Gut Microflora 675
The Role of Epigenetic Mechanisms 587 Microbiome, Epigenetics, and Effect on Metabolism 675
Conclusion 595 Gut microbiota, Inflammation, and Colorectal
Summary 595 Carcinogenesis 677
x Contents

Pathogenic Infections and Cancer 677 Type 1 Diabetes Mellitus 724

Pathogenic Infections and Epigenetic Modifications 680 Systemic Sclerosis 725
Summary 683 Use of Epigenetic Modifications as Potential
References 683 Biomarkers 726
Use of Epigenetic Modifiers for Potential Diagnosis and
Therapy in Autoimmune Diseases 727
Summary 728
34. Population Pharmacoepigenomics 687 Multiomics and machine learning accurately predict
JACOB PEEDICAYIL clinical response to adalimumab and etanercept
therapy in patients with rheumatoid arthritis [203] [ex:
Introduction 687 Autoimmunity Epigenetics Case Study] 728
General Aspects of Population Pharmacoepigenomics 688 References 730
Population Variations of Epigenetic Patterns and
Population Pharmacoepigenomics 688
Human Epigenome Projects and Population
Pharmacoepigenomics 688 37. Epigenetics of Brain Disorders 737
Population Pharmacoepigenomics in Relation to ALI JAWAID, ELOÏSE A. KREMER, NANCY V.N. CARULLO AND
Pharmacokinetics 689 ISABELLE M. MANSUY
Population Pharmacoepigenomics in Relation to
Pharmacodynamics 689 Introduction 738
3D and 4D Chromatin Structures in the Nuclei of Cells Important Epigenetic Mechanisms for the Brain 738
in the Liver and Other Body Organs and Population Epigenetic Dysregulation in Neurodevelopmental
Pharmacoepigenomics 690 Disorders: The Example of Rett Syndrome 739
Population Pharmacoepigenomics in Relation to Epigenetic Dysregulation in Neurodegenerative
Adverse Drug Reactions and Drug Interactions 691 Disorders: The Example of Alzheimer’s Disease 742
Conclusions 691 Epigenetic Dysregulation in Psychiatric Disorders:
Population Pharmacoepigenomics Case Study 691 The Example of Depression 745
References 693 Epigenetic Dysregulation by Environmental Stress:
The Example of Early-life Stress 748
Conclusions and Outlook 749
VIII Summary
Research case study
750
751
Epigenetics and Human Disease Acknowledgments 752
References 752

35. Cancer Epigenetics 697

MARINA ALEXEEVA, MARCUS ROALSØ AND KJETIL SØREIDE 38. Epigenetics of Metabolic Diseases 761
LINN GILLBERG AND LINE HJORT
Introduction 697
Epigenetic Influences Over a Lifetime and Cancer Risk 698 Introduction 761
Epigenetics in Cancer: Remodelers, Writers, Readers, and Impact of Age and Lifestyle Factors on the Epigenome 762
Erasers 699 Epigenetic Memory, Prenatal Exposure, and Risk of
Genetic and Epigenetic Classification of Cancer 705 Metabolic Disease 766
Epigenetic Biomarkers in Cancer 708 Epigenetic Features of Metabolic Diseases 769
Epigenetics as Cancer Therapeutic Targets 709 Conclusions 771
Future Perspectives 710 References 772
References 711

39. Imprinting Disorders in Humans 779

36. The Role of Epigenetics in Autoimmune
THOMAS EGGERMANN
Disorders 715
KERSTIN KLEIN Introduction 779
Clinical Findings in Imprinting Disorders 779
Epigenetic Mechanisms Influence Autoimmune Processes 715 Molecular Findings in Imprinting Disorders 781
Mechanisms of Autoimmunity 716 Causes of Disturbed Imprinting 782
Epigenetics of Immune Cells 719 Cis-acting Factors 783
Epigenetics of Systemic Lupus Erythematosus 720 Trans-acting Factors 784
Epigenetics of Rheumatoid Arthritis 722 Maternal Effect Mutations and Multilocus Imprinting
Multiple Sclerosis 723 Disturbance 784
 Contents xi
Translational Use of New Findings in ImpDis and New Chromatin-remodeling Agents, Combined Treatment, and
Methodologies 785 Targeted Therapy 822
Genetic and Reproductive Counseling 787 DNA Methylation/Demethylation and Combined Treatment 823
Clinical Management 787 Histone Modifications and Histone-modifying Enzymes for
Concluding Remarks 787 Epigenetic Treatment 828
References 787 Conclusions and Future Perspectives 833
Clinical Trial 833
References 837
IX
Epigenetic Therapy
X
40. Clinical Applications of Histone Deacetylase The Future of Epigenetics
Inhibitors 793
ROMAIN PACAUD, JOSE GARCIA, SCOTT THOMAS AND
PAMELA N. MUNSTER
42. New Directions for Epigenetics:
Application of Engineered DNA-binding
Introduction 793 Molecules to Locus-specific Epigenetic Research 843
HDACi for the Treatment of Hematological Malignancies 795
TOSHITSUGU FUJITA AND HODAKA FUJII
HDACi in the Treatment of Solid Tumors 801
Clinical Applications of HDACi for Noncancer Diseases 807 Introduction 843
Conclusions and the Future Directions of the Clinical General Information on Engineered DNA-binding
Applications of HDACi 809 Molecules 844
References 810 Locus-specific Epigenome Editing 845
Locus-specific Identification of Epigenetic Molecules
that Interact with Target Genomic Regions 858
41. Combination Epigenetic Therapy 821
Conclusions 862
RŪTA NAVAKAUSKIENĖ References 862
Introduction 821 Index 869
 List of contributors
Nobuyoshi Akimitsu Isotope Science Center, The
University of Tokyo, Tokyo, Japan
Marina Alexeeva Department of Gastrointestinal Surgery,
Stavanger University Hospital, Stavanger, Norway;
Gastrointestinal Translational Research Unit, Laboratory
for Molecular Biology, Stavanger University Hospital,
Stavanger, Norway
Juliana Almeida Centre of Natural Sciences and
Humanities, Federal University of ABC, Sao Bernardo do
Campo, Brazil
Rodolfo Daniel Ávila-Avilés Laboratory of Epigenetics of
Skeletal Muscle Regeneration, Department of Genetics
and Molecular Biology, Centre for Research and
Advanced Studies-IPN, Mexico City, Mexico
Jérémy Berthelier Plant Epigenetics Unit, Okinawa
Institute of Science and Technology Graduate University,
Onna-son, Okinawa, Japan
Akanksha Bhatnagar Department of Biology, Drexel
University, Philadelphia, PA, United States
Maria Boskovic Laboratory for Cancer Research,
University of Split School of Medicine, Split, Croatia
Nancy V.N. Carullo Laboratory of Neuroepigenetics,
Brain Research Institute, Medical Faculty of the University
of Zurich, Zurich, Switzerland; Zurich Neuroscience
Center, ETH and University of Zurich, Zurich,
Switzerland
J. Armando Casas-Mollano BioTechnology Institute,
University of Minnesota, Twin-Cities, Saint Paul, MN,
United States
Frances A. Champagne Department of Psychology,
University of Texas, Austin, TX, United States
Taiping Chen The Ministry of Education Key Laboratory
of Laboratory Medical Diagnostics, College of Laboratory
Medicine, Chongqing Medical University, Chongqing, P.
R. China
Ravindresh Chhabra Department of Biochemistry, Central
University of Punjab, Ghudda, Punjab, India
James P. Curley Department of Psychology, University of
Texas, Austin, TX, United States
Gareth W. Davison Faculty of Life and Health Sciences,
Ulster University, Northern Ireland, United Kingdom
Gary L. Dunbar Field Neurosciences Institute, Saginaw,
MI, United States
Thomas Eggermann Institut für Humangenetik, RWTH
Aachen, Aachen, Germany
xiii
Felice Elefant Department of Biology, Drexel University,
Philadelphia, PA, United States
Peter D. Fransquet School of Public Health and Preventive
Medicine, Monash University, Melbourne, VIC, Australia
Hodaka Fujii Department of Biochemistry and Genome
Biology, Hirosaki University Graduate School of
Medicine, Aomori, Japan
Toshitsugu Fujita Department of Biochemistry and
Genome Biology, Hirosaki University Graduate School of
Medicine, Aomori, Japan
Leonardo Furci Plant Epigenetics Unit, Okinawa Institute
of Science and Technology Graduate University, Onna-
son, Okinawa, Japan
Jose Garcia Division of Hematology and Oncology,
University of California, San Francisco, CA, United States
Balaram Ghosh Epigenetic Research Laboratory,
Department of Pharmacy, Birla Institute of Technology
and Science-Pilani Hyderabad Campus, Shamirpet,
Hyderabad, Telangana, India
Linn Gillberg Department of Biomedical Sciences,
University of Copenhagen, Copenhagen, Denmark
Karen Giménez-Orenga Centro de Investigación
Traslacional San Alberto Magno, Universidad Católica de
Valencia San Vicente Mártir, Valencia, Spain
Courtney W. Hanna Centre for Trophoblast Research,
University of Cambridge, Cambridge, United Kingdom;
Department of Physiology, Development and
Neuroscience, University of Cambridge, Cambridge,
United Kingdom; Epigenetics Programme, Babraham
Institute, Cambridge, United Kingdom
Zdenko Herceg International Agency for Research on
Cancer (IARC), Lyon, France
J. Manuel Hernández-Hernández Instituto Politécnico
Nacional 2508, San Pedro Zacatenco, Ciudad de México,
México
Line Hjort Department of Endocrinology, Copenhagen
University Hospital, Copenhagen, Denmark
Xiaotong Hu Sir Run Run Shaw Hospital, Zhejiang
University, Hangzhou, Zhejiang, P.R. China
Eveline M. Ibeagha-Awemu Sherbrooke Research and
Development Centre, Agriculture and Agri-Food Canada,
Sherbrooke, QC, Canada
Ali Jawaid Laboratory of Neuroepigenetics, Brain Research
Institute, Medical Faculty of the University of Zurich,
Zurich, Switzerland; Department of Health Sciences and
xiv List of contributors
Technology, Institute for Neuroscience, ETH Zurich,
Zurich, Switzerland; Zurich Neuroscience Center, ETH
and University of Zurich, Zurich, Switzerland
Wei Jiang Frontier Science Center for Immunology and
Metabolism, Medical Research Institute, Wuhan
University, Wuhan, P.R. China
Oscar Juez Plant Epigenetics Unit, Okinawa Institute of
Science and Technology Graduate University, Onna-son,
Okinawa, Japan
Ashley M. Karnay Department of Neurobiology &
Anatomy, Drexel University College of Medicine,
Philadelphia, PA, United States
Kentaro Kawata Isotope Science Center, The University of
Tokyo, Tokyo, Japan; Cellular and Molecular
Biotechnology Research Institute, National Institute of
Advanced Industrial Science and Technology (AIST),
Tokyo, Japan
Hasan Khatib Department of Animal and Dairy Sciences,
University of Wisconsin, Madison, WI, United States
Eric W. Klee Division of Computational Biology,
Department of Quantitative Health Sciences, Mayo Clinic,
Rochester, MN, United States
Kerstin Klein Department of BioMedical Research,
University of Bern, Bern, Switzerland; Department of
Rheumatology and Immunology, Bern University
Hospital, Bern, Switzerland
Eloı̈se A. Kremer Laboratory of Neuroepigenetics, Brain
Research Institute, Medical Faculty of the University of
Zurich, Zurich, Switzerland; Zurich Neuroscience Center,
ETH and University of Zurich, Zurich, Switzerland
Ilkka Kronholm Department of Biological and
Environmental Science, University of Jyväskylä,
Jyväskylä, Finland
Ho-Sun Lee Interdisciplinary Program in Bioinformatics
and Department of Statistics, Seoul National University,
Seoul, Republic of Korea; Toxicology Division, National
Forensic Service Daegu Institute, Republic of Korea
Frédérique Magdinier Aix Marseille Univ, INSERM,
Marseille Medical Genetics, MMG, Marseille, France
Isabelle M. Mansuy Laboratory of Neuroepigenetics, Brain
Research Institute, Medical Faculty of the University of
Zurich, Zurich, Switzerland; Zurich Neuroscience Center,
ETH and University of Zurich, Zurich, Switzerland
Rahia Mashoodh Department of Zoology, University of
Cambridge, Cambridge, United Kingdom
Mihaly Mezei Department of Pharmaceutical Sciences,
Icahn School of Medicine at Mount Sinai, New York, NY,
United States
Maria Miah Department of Biology, Medgar Evers College,
City University of New York, Brooklyn, NY, United States
Matin Miryeganeh Plant Epigenetics Unit, Okinawa
Institute of Science and Technology Graduate University,
Onna-son, Okinawa, Japan
Shiraz Mujtaba Department of Biology, Medgar Evers
College, City University of New York, Brooklyn, NY,
United States
Pamela N. Munster Division of Hematology and Oncology,
University of California, San Francisco, CA, United States
Rabih Murr Faculty of Medicine, Department of Genetic
Medicine and Development, University of Geneva,
Geneva, Switzerland
Rūta Navakauskienė Life Sciences Center, Vilnius
University, Vilnius, Lithuania
Claudia Negrón-Lomas Laboratory of Epigenetics of
Skeletal Muscle Regeneration, Department of Genetics
and Molecular Biology, Centre for Research and
Advanced Studies-IPN, Mexico City, Mexico
Fereshteh S. Nugent Department of Pharmacology &
Molecular Therapeutics, F. Edward Hebert School of
Medicine, Uniformed Services University of the Health
Sciences, Bethesda, MD, United States
Elisa Oltra Centro de Investigación Traslacional San
Alberto Magno, Universidad Católica de Valencia San
Vicente Mártir, Valencia, Spain; Department of Pathology,
School of Medicine and Health Sciences, Universidad
Católica de Valencia San Vicente Mártir, Valencia, Spain
Rena Onoguchi-Mizutani Isotope Science Center, The
University of Tokyo, Tokyo, Japan
Nail Can Öztürk Department of Anatomy, Mersin
University, Mersin, Turkey
Romain Pacaud Division of Hematology and Oncology,
University of California, San Francisco, CA, United States
Jacob Peedicayil Department of Pharmacology & Clinical
Pharmacology, Christian Medical College, Vellore, Tamil
Nadu, India
Prasad Pethe Symbiosis Centre for Stem Cell Research
(SCSCR), Symbiosis International University (SIU), Pune,
Maharashtra, India
Gerd P. Pfeifer Department of Epigenetics, Van Andel
Institute, Grand Rapids, MI, United States
Sravani Pulya Epigenetic Research Laboratory, Department
of Pharmacy, Birla Institute of Technology and Science-
Pilani Hyderabad Campus, Shamirpet, Hyderabad,
Telangana, India
Tibor A. Rauch University of Pécs Medical School, Pécs,
Hungary
Marisol Resendiz Stark Neuroscience Research Institute
Indiana University School of Medicine, Indianapolis, IN,
Uinted States
Marcus Roalsø Department of Gastrointestinal Surgery,
Stavanger University Hospital, Stavanger, Norway;
Gastrointestinal Translational Research Unit, Laboratory
for Molecular Biology, Stavanger University Hospital,
Stavanger, Norway; Department of Quality and Health
Technology, University of Stavanger, Stavanger Norway
Jérôme D. Robin Aix Marseille Univ, INSERM, Marseille
Medical Genetics, MMG, Marseille, France
Julien Rossignol Central Michigan University, Mt.
Pleasant, MI, United States
Joanne Ryan School of Public Health and Preventive
Medicine, Monash University, Melbourne, VIC, Australia
 List of contributors
Cı́ntia Barros Santos-Rebouças Department of Genetics,
Institute of Biology Roberto Alcantara Gomes, State
University of Rio de Janeiro, Rio de Janeiro, Rio de
Janeiro, Brazil
Hidetoshi Saze Plant Epigenetics Unit, Okinawa Institute
of Science and Technology Graduate University, Onna-
son, Okinawa, Japan
Ryan D. Shepard Department of Pharmacology &
Molecular Therapeutics, F. Edward Hebert School of
Medicine, Uniformed Services University of the Health
Sciences, Bethesda, MD, United States; Synapse and
Neural Circuit Research Section, National Institute of
Neurological Disorders and Stroke, National Institutes of
Health, Bethesda, MD, United States
Philippe Silar Université de Paris, Paris Cité, France
Athena Sklias Center for Integrative Genomics, University
of Lausanne, Lausanne, Switzerland
Susan L. Slager Division of Computational Biology,
Department of Quantitative Health Sciences, Mayo Clinic,
Rochester, MN, United States
Kjetil Søreide Department of Gastrointestinal Surgery,
Stavanger University Hospital, Stavanger, Norway;
Gastrointestinal Translational Research Unit, Laboratory
for Molecular Biology, Stavanger University Hospital,
Stavanger, Norway; Department of Clinical Medicine,
University of Bergen, Bergen, Norway
Bhairavi Srinageshwar Central Michigan University, Mt.
Pleasant, MI, United States
David M. Suter Institute of Bioengineering, School of Life
Sciences, Swiss Federal Institute of Technology (EPFL),
Lausanne, Switzerland
Kenzui Taniue Isotope Science Center, The University of
Tokyo, Tokyo, Japan
Scott Thomas Division of Hematology and Oncology,
University of California, San Francisco, CA, United States
Shulan Tian Division of Computational Biology,
Department of Quantitative Health Sciences, Mayo Clinic,
Rochester, MN, United States
Trygve O. Tollefsbol Department of Biology, University of
Alabama at Birmingham, Birmingham, AL, United States;
O’Neal Comprehensive Cancer Center, University of
Alabama at Birmingham, Birmingham, AL, United States;
Integrative Center for Aging Research, University of
Alabama at Birmingham, Birmingham, AL, United States;
xv
Nutrition Obesity Research Center, University of Alabama
at Birmingham, Birmingham, AL, United States;
Comprehensive Diabetes Center, University of Alabama
at Birmingham, Birmingham, AL, United States;
University Wide Microbiome Center, University of
Alabama at Birmingham, Birmingham, AL, United States
Mark van der Giezen Department of Chemistry, Bioscience
and Environmental Engineering, University of Stavanger,
Stavanger, Norway; Biosciences, University of Exeter,
Exeter, United Kingdom
Ludovica Vanzan Institute of Bioengineering, School of
Life Sciences, Swiss Federal Institute of Technology
(EPFL), Lausanne, Switzerland
Günter Vogt Faculty of Biosciences, University of
Heidelberg, Heidelberg, Germany
Darryl S. Watkins Stark Neuroscience Research Institute
Indiana University School of Medicine, Indianapolis, IN,
Uinted States
Martin M. Watson Department of Chemistry, Bioscience
and Environmental Engineering, University of Stavanger,
Stavanger, Norway
Loo Keat Wei Faculty of Science, Department of Biological
Science, Universiti Tunku Abdul Rahman, Kampar, Perak,
Malaysia
Jo Wrigglesworth School of Public Health and Preventive
Medicine, Monash University, Melbourne, VIC, Australia
Toshimichi Yamada Isotope Science Center, The University
of Tokyo, Tokyo, Japan
Huihuang Yan Division of Computational Biology,
Department of Quantitative Health Sciences, Mayo Clinic,
Rochester, MN, United States
Jie Yang Frontier Science Center for Immunology and
Metabolism, Medical Research Institute, Wuhan
University, Wuhan, P.R. China
Zhengzhou Ying Department of Epigenetics and Molecular
Carcinogenesis, The University of Texas MD Anderson
Cancer Center, Houston, TX, United States
Ericka Zacarias BioTechnology Institute, University of
Minnesota, Twin-Cities, Saint Paul, MN, United States
Feng C. Zhou Stark Neuroscience Research Institute
Indiana University School of Medicine, Indianapolis, IN,
Uinted States; Department of Anatomy, Cell Biology and
Physiology, IUSM, Indianapolis, IN, Uinted States
 S E C T I O N I

Overview

1. Epigenetics overview
This page intentionally left blank
 C H A P T E R

1
Epigenetics Overview
Trygve O. Tollefsbol1,2,3,4,5,6
1
Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States 2O’Neal
Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States 3Integrative
Center for Aging Research, University of Alabama at Birmingham, Birmingham, AL, United States 4Nutrition Obesity
Research Center, University of Alabama at Birmingham, Birmingham, AL, United States 5Comprehensive Diabetes
Center, University of Alabama at Birmingham, Birmingham, AL, United States 6University Wide Microbiome Center,
University of Alabama at Birmingham, Birmingham, AL, United States

O U T L I N E

Introduction 3 Epigenetic Epidemiology 6

Molecular Mechanisms of Epigenetics 3 Epigenetics and Human Disease 7
Methods in Epigenetics 4 Epigenetic Therapy 7
Model Organisms of Epigenetics 5 The Future of Epigenetics 7
Factors Influencing Epigenetic Changes 5 Conclusion 8
Evolutionary Epigenetics 6 References 8

INTRODUCTION MOLECULAR MECHANISMS OF

In 1942, Conrad Waddington first defined epige-
netics as the causal interactions between genes and
their products that allow for the phenotypic expression
[1]. This term has now been somewhat redefined and
although there are many variants of the definition
today, a consensus definition is that epigenetics is the
collective heritable changes in phenotype due to pro-
cesses that arise independent of changes in the pri-
mary DNA sequence. This heritability of epigenetic
information was for many years thought to be limited
to mitotic cellular divisions. However, it is now appar-
ent that epigenetic processes can be transferred meioti-
cally in organisms from one generation to another
[2,3]. This phenomenon was first described in plants
[4] and has been expanded to include yeast, Drosophila,
mouse, and possibly humans [5 7].
EPIGENETICS
DNA methylation is the most studied of epigenetic
processes. It most eukaryotes, DNA methylation
consists of transfer of a methyl moiety from
S-adenosylmethionine (SAM) to the 5-position of cyto-
sines in certain CpG dinucleotides. This important
enzymatic transfer reaction is catalyzed by the DNA
methyltransferases (DNMTs). The three major DNMTs
are DNMT1, 3A, and 3B. DNMT1 catalyzes what is
called maintenance methylation, which occurs during
each cellular replication as the DNA duplicates. The
other major DNMTs, 3A and 3B, are characterized by
their relatively higher de novo methylation activity.
This process leads to the introduction of
5-methylcytosines (5mCs) into the genome at sites that
were not previously methylated. Notably, the most

Handbook of Epigenetics.
DOI: https://doi.org/10.1016/B978-0-323-91909-8.00031-1 3 Copyright © 2023 Elsevier Inc. All rights reserved.
4 1. EPIGENETICS OVERVIEW
significant aspect of DNA methylation, which can also
influence such processes as X-chromosome inactivation
and cellular differentiation, is its effects on gene
expression. In general, the more methylated a
gene regulatory region, the more likely it is that the
gene activity will become downregulated and vice ver-
sa, although there are some exceptions to this dogma
[8]. Chapter 2 of this book reviews the mechanisms of
DNA methylation and demethylation during mamma-
lian development. Major changes in DNA methylation
occur during development and this is especially true
with respect to early embryonic development. Further,
the germ cells also display many changes during
gametogenesis. Recent advances have highlighted
important roles of the ten-eleven translocation family
of dioxygenases. These enzymes convert 5mC to
5-hydroxymethylcytosie (5hmC), 5-formylcytosine
(5fC), and 5-carboxylcytosine (5caC) and appear to
play important roles in the dramatic DNA demethyla-
tion that occurs during early development. The 5mC
oxidized derivatives may also serve as epigenetic
marks that modulate chromatin regulation.
There are additional important epigenetic changes
that occur in the genome. For example, chromatin
changes are another central epigenetic process that
have an impact not only on gene expression, but also
many other biological processes. Posttranslational
modifications of histones such as acetylation and
methylation occur in a site-specific manner and often
influence the binding and activities of other proteins
that influence gene regulation. The histone acetyltrans-
ferases catalyze histone acetylation and the histone
deacetylases (HDACs) result in removal of acetyl
groups from key histones that comprise the chromatin.
These modifications can occur at numerous sties in the
histones and are most common in the amino terminal
regions of these proteins as discussed in Chapter 3. In
general, increased histone acetylation is associated
with greater gene activity and vice versa. Methylation
of histones has variable effects on gene activity. Lysine
4 (K4) methylation of histone H3 is often associated
with increasing gene activity whereas methylation of
lysine 9 (K9) of histone H3 may lead to transcriptional
repression. There is also considerable crosstalk
between DNA methylation and histone modifications
[9] such that cytosine methylation may increase the
likelihood of H3K9 methylation and H3K9 methylation
may promote cytosine methylation. In addition,
histone-modifying epigenetic enzymes have recently
been identified that may have key roles that are not
dependent on their catalytic activity (Chapter 3).
Among the most exciting advances in epigenetics
have been the discoveries of many other processes
besides DNA methylation, and histone modifications
impacting the epigenetic behavior of cells. RNA is highly
I. OVERVIEW
versatile and often plays a major role in epigenetic pro-
cesses. For instance, noncoding RNA (Chapter 4) includ-
ing both short (,200 nucleotides) and long ( . 200
nucleotides) forms, often share protein and RNA compo-
nents with the RNA interference (RNAi) pathway and
they may also influence more conventional aspects of
epigenetics such as DNA methylation and chromatin
marking. These effects appear to be wide-spread and
occur in organisms ranging from protists to humans.
Notably, the noncoding RNAs may serve as therapeutic
targets for a number of human diseases and this area of
epigenetics is now attracting considerable attention.
Prions are fascinating in that they can influence epige-
netic processes independent of DNA and chromatin. In
Chapter 5 it is shown that structural heredity also is
important in epigenetic expression where alternative
states of macromolecular complexes or regulatory net-
works can have a major effect on phenotypic expression
independent of changes in DNA sequences. The prion
proteins are able to switch their structure in an autocata-
lytic manner that can not only influence epigenetic
expression, but also lead to human disease although the
full potential of prions in epigenetic processes is still on
the horizon.
The position of a gene in a given chromosome can
also greatly influence its expression (Chapter 6). Upon
rearrangement, a gene may be relocated to a hetero-
chromatic region of the genome leading to gene silenc-
ing. Moreover, a change in position of a regulatory
element may affect the maintenance of chromatin
architecture and subsequently cellular functioning.
Polycomb mechanisms are another aspect of epige-
netics that control all of the major cellular differentia-
tion pathways and are also involved in cell fate.
Polycomb protein repression is very dynamic and can
be easily reversed by activators. They also raise the
threshold of the signals or activators required for tran-
scriptional activation which places these fascinating
proteins within the realm of epigenetic processes.
Polycomb complexes can generate H2A ubiquitylation
and H3K27 methylation that often mediate their
repressive functions and H3K27 may serve as an epi-
genetic memory for Polycomb repression as described
in Chapter 7. Therefore, although DNA methylation
and histone modifications are mainstays of epigenetics,
recent advances have greatly expanded the field of epi-
genetics to include many other processes such as non-
coding RNA, prions, chromosome position effects and
Polycomb mechanisms.
METHODS IN EPIGENETICS
Numerous advances in epigenetics that have driven
this field for the past two decades can be traced back
 FACTORS INFLUENCING EPIGENETIC CHANGES
to the technological breakthroughs that have made the
many discoveries possible. We now have a wealth of
information about key gene-specific epigenetic changes
that occur in a myriad of biological processes.
However, among the most exciting advances have
been important breakthroughs in analyses of the
methylome at high resolution. High-throughput
sequencing, which has largely replaced microarray
platforms, has made possible new techniques to ana-
lyze genome-wide features of epigenetics that are
based on uses of methylation-sensitive restriction
enzymes, sodium bisulfite conversion and affinity cap-
ture with antibodies or proteins that select methylated
DNA sequences. Tiling arrays may be employed for
analysis of chromosomal segments or the whole
genome and whole genome high-throughput sequenc-
ing is now a staple for reliable and specific methylomic
analyses. Additionally, single-cell analyses of DNA
methylation patterns by whole genome epigenetic
analyses are emerging as described in Chapter 8.
Chromatin immunoprecipitation and sequencing
(ChIP-seq) is frequently used in epigenetic analyses
and can also be applied to single cells as well as used
for mapping two modifications simultaneously as
described in Chapter 9. Likewise, genome-wide
expression analyses of RNAs have been made possible
with RNA-seq that allows detection of a myriad of
noncoding RNAs (Chapter 10). Since there has been
much information derived from epigenomic
approaches, methods to analyze data from ChIP-seq
and RNA-seq, for example, are becoming increasingly
important and are delineated in Chapter 11. Notably,
developments in the tools for assessing epigenetic
information have been and will continue to be an
important driving force in advancing epigenetics.
MODEL ORGANISMS OF EPIGENETICS
Epigenetic processes are wide-spread and much of
our extant knowledge about epigenetics has been
derived from model systems, both typical and unique.
The ease of manipulation of prokaryotic organisms has
facilitated discoveries in the molecular mechanisms of
basic epigenetic processes. Although prokaryotic
organisms do not contain chromatin, some bacteria are
capable of encoding factors which lead to posttransla-
tional modifications of an epigenetic nature as
described in Chapter 12. Drosophila is a mainstay
model in biology in general and the epigenetics field is
not an exception in this regard. For example,
Chapter 13 discusses how use of Drosophila as a model
organism has significantly increased knowledge of
chromatin organization and may have powerful poten-
tial in facilitating understanding of the epigenetics of
I. OVERVIEW
5
neurological disorders. Perhaps the most useful model
system in epigenetics to date is the mouse model
(Chapter 14). Numerous different mouse models have
been developed that are important in many different
epigenetic processes such as transgenerational epige-
netics and imprinting and these models have potential
in illuminating a number of human diseases. Analyses
of epigenetic processes in development and health of
offspring can also be facilitated through the use of
mouse models. Plant models (Chapter 15) are of great
importance in epigenetics due in part to their plasticity
and their ability to silence transposable elements.
RNAi silencing in plants has been at the forefront of
epigenetics and plant models will likely lead the way
in several other epigenetic processes in the future. Use
of plant models has also facilitated the development of
targeted epigenome editing in plants that may have
great significance in enhancing crop performance.
Thus, model development, like the advances in techni-
ques, have made many of the most exciting discoveries
in epigenetics possible for a number of years.
FACTORS INFLUENCING EPIGENETIC
CHANGES
The functions of epigenetics are indeed numerous
and it would be next to impossible to do complete jus-
tice in one book to this ever-expanding field. However,
Chapters 16 25 illustrate a few of the many different
functions that epigenetics mediates. For example,
Chapter 16 reviews the role of epigenetics in early
development and illustrates that both gene-specific
and global changes in DNA methylation are central to
embryonic development. In addition, perturbations
mediated by processes such as stress during develop-
ment may lead to disease formation later in life.
Chapter 17 reviews epigenetic biomarkers that are also
very important and serve the key function of inform-
ing the staging and classification of disease as well as
guiding clinical management. Another factor that can
significantly influence epigenetic changes is the activ-
ity of transposable elements. These elements insert into
coding or noncoding regions of the genome and can
also exert effects in cis by their insertion or altering of
the epigenetic state of the insertional site itself as
described in Chapter 18. These mechanisms of trans-
posable elements have not only shaped evolution, but
can also contribute to epigenetic-based diseases.
Epigenetics is intricately linked to changes in the
metabolism of organisms and these two processes can-
not be fully understood separately. SAM is a universal
methyl donor and drives many epigenetic processes;
the importance of SAM in epigenetic mechanisms is
vast. Metabolic functions can also influence the
6 1. EPIGENETICS OVERVIEW
chromatin which is a major mediator of epigenetic pro-
cesses (Chapter 19). It is now apparent that various
environmental influences such as diet and changes in
metabolic compounds can regulate the many enzymes
that modify histones in mammals. Thus, metabolic
processes impacted by dietary changes can greatly
influence both DNA methylation and chromatin remo-
deling, the two major epigenetic mediators, and signif-
icantly influence gene regulation in both health and
disease.
Stem cells rely in part on signals from the environ-
ment and epigenetic mechanisms have central roles in
how stem cells respond to environmental influences
(Chapter 20) and how therapeutic roles of stem cells
may contribute to management of many diseases such
as multiple sclerosis, Huntington disease and Parkinson
disease. Regenerative medicine is dependent upon stem
cells. Regulation of muscle regenerative abilities
involves key changes in the epigenome that regulate
gene expression and may have potential use to treat
skeletal muscle diseases (Chapter 21). Some of the basic
tenets of epigenetics were first realized through studies
of X-chromosome inactivation which allows for dosage
compensation for X-linked gene expression between
males and females. As discussed in Chapter 22,
advances in the study of the epigenetics of X-
chromosome inactivation have revealed that epigenetic
modification of the inheritance mode of X-driven phe-
notypes can impact the plasticity of human conditions
and may lead to new strategies for treating dominant
X-linked disorders in females. Profound new discover-
ies have occurred in the area of the epigenetics of mem-
ory processes. Recent exciting discoveries have shown
that gene regulation through epigenetic mechanisms is
necessary for changes in adult brain function and
behavior based on life experiences (Chapter 23).
Moreover, new drugs that impact epigenetic mechan-
isms may have future uses in treating or alleviating cog-
nitive dysfunction. Transgenerational inheritance
(Chapter 24) is also a form of memory based in part on
epigenetics in that early life experiences that impact
epigenetic markers can greatly influence adult health
and risk for diseases. In addition, the aging process
is a form of epigenetic memory and experience in
that our genes are epigenetically modified from our
parents as well as during our entire life spans that
can significantly impact the longevity of humans as
well as our risk for the many age-related diseases,
many of which are also epigenetically based. As
reviewed in Chapter 25, there has been a surge of
interest in DNA methylation biomarkers of aging
which are referred to as “epigenetic clocks.”
Environmental factors have been found to influence
these epigenetic biomarkers and they have consider-
able potential for identifying accelerated epigenetic
I. OVERVIEW
aging, certain epigenetic-based diseases, and may
have prognostic capacity for age-related diseases. It
is therefore apparent that epigenetics influences
numerous different functions and it is highly likely
that many additional functions of epigenetics will be
discovered in the future.
EVOLUTIONARY EPIGENETICS
Although many think of epigenetic processes as
being inherent and static to a specific organism, it is
apparent that epigenetics have been a major force
behind the evolutionary creation of new species.
Chapter 26 reveals that epigenetic mediators such as
H3K4 and H3K27 methyltransferases have significantly
impacted plant evolution. The expansion of gene fami-
lies of these enzymes may have allowed for changes in
chromatin regulation of new genes and pathways that
have modified plant evolution. The epigenetic machin-
ery has also played a major role in the evolution of ani-
mals. As described in Chapter 27, DNA methylation
may serve as a driver of evolution through its effects
on gene regulation. Vertebrates have evolved genome-
wide methylation while invertebrates are characterized
by mosaic DNA methylation patterns. Epigenotype
diversification followed by genetic fixation could be a
major mechanism of evolution that is currently under-
studied and may receive increasing attention in future
analyses of epigenetics in evolutionary processes.
Adaptive evolution by natural selection requires heri-
tability, and spontaneous epigenetic changes may have
been important in adaptive evolution, although there
are important differences between genetic variation
and epigenetic variation with respect to supply and
stability of epigenetic mutations (Chapter 28).
EPIGENETIC EPIDEMIOLOGY
A very new and exciting area within the field of epi-
genetics is the impact of epigenetic mechanisms on
livestock breeding. Chapter 29 indicates that the breed-
ing programs of livestock that are currently in place
account for only part of the phenotypic variance in
traits and that epigenetic factors of variance need fur-
ther consideration. In fact, livestock epigenetics may
have a major impact on the growth and development
of livestock and profoundly affect phenotypic out-
comes. Dietary factors are highly variable not only
between individuals but also among human popula-
tions and various nonhuman species. Many studies
have shown that the diet has a profound effect on the
epigenetic expression of the genome and therefore
on the phenotype. An important example of this
 THE FUTURE OF EPIGENETICS
phenomenon is the link between the nutritional epi-
genome and fetal metabolic programming (Chapter 30)
in that early epigenetic changes through nutritional
means may exacerbate the risk of development of vari-
ous metabolic conditions later in life. Another factor
besides diet that can impact the epigenome is abused
use of drugs that induce epigenomic aberrations which
are features of drug addiction. Drugs of abuse are also
able to recruit epigenetic mechanisms that can impact
the reward circuitry which is of central interest in drug
abuse as reviewed in Chapter 31. It is possible that
modifications of the epigenetic circuitry in cases of
chronic drug abuse may lead to therapeutic options of
those addicted to certain drugs. Other environmental
agents can also greatly impact the epigenome. For
example, Chapter 32 reviews the many environmental
agents that can lead to alterations in the epigenome
thereby inducing toxicity or carcinogenesis. The envi-
ronment also affects the gut microbiome (Chapter 33)
which is known to modulate epigenetic processes. An
increased understanding of the dynamic interactions
between the gut microbiome and epigenetic modifica-
tions may have considerable translational potential.
Drugs besides those of addiction can also reshape the
epigenome which has opened the new field of pharma-
coepigenomics. It is clear that certain populations
respond differently to drugs, and much of this varia-
tion may be explained by epigenetic factors
(Chapter 34). Thus, epidemiological factors have great
importance in epigenetics and this is influenced by
diet, addictive drugs, environmental agents, the gut
microbiome, other drugs besides those of addiction,
and likely many other factors as well.
EPIGENETICS AND HUMAN DISEASE
A major interest in epigenetics stems from the role
of epigenetic changes in the etiology, progression, and
diagnosis of human diseases. Cancer has long been
associated with epigenetic alterations and DNA meth-
ylation, chromatin modifications, and RNA-dependent
regulation have all been shown to affect the incidence
and severity of cancer (Chapter 35). Many immune dis-
orders such as systemic lupus erythematosus and
rheumatoid arthritis, as well as multiple sclerosis,
have been associated with epigenetic aberrations
(Chapter 36); epigenetic processes have also been
linked to brain disorders (Chapter 37). In the latter
case, the Rett syndrome, Alzheimer disease and
Huntington disease have been associated in at least
some way with epigenetic alterations. Even schizo-
phrenia and depression may have an epigenetic basis
in their expression. However, system metabolic disor-
ders may also be related to epigenetic aberrations. For
I. OVERVIEW
7
example, obesity, gestational diabetes, and hyperten-
sion can influence the fetal chromatin and lead to an
increased incidence in adult disease later in life
(Chapter 38). Since genomic imprinting is based on
epigenetic mechanisms, it may come as no surprise
that defects in imprinting can lead to a number of
human diseases (Chapter 39). The Prader-Willi syn-
drome, Angelman syndrome, Silver Russell syndrome,
and transient neonatal diabetes mellitus, are all due to
imprinting disorders that are based on epigenetic
defects. Therefore, the number of diseases impacted by
epigenetic processes is large and advances in the treat-
ment of these disorders will likely depend in part on
breakthroughs in epigenetic therapy.
EPIGENETIC THERAPY
Although there are many epigenetic therapies that
are in use and on the horizon, histone-modifying
drugs have probably received the most attention in the
clinics. Chief among these are the histone deacetylase
(HDAC) inhibitors. Vorinostat (Zolinza), for example,
has been approved by the US Food and Drug
Administration for use in the treatment of patients
with cutaneous T-cell lymphoma (Chapter 40). Many
different HDAC inhibitors have been developed, and it
is likely that significant improvements will occur for
HDAC inhibitors as well as many other drugs that can
normalize aberrations in not only histone modifica-
tions, but also DNA methylation and perhaps some of
the many other epigenetic processes that have been
discovered. On the horizon is an increasing interest in
combinatorial approaches using epigenetic-modifying
agents with other forms of therapy. Moreover, as
described in Chapter 41, the combined use of
epigenetic-modifying drugs such as DNA methylation
and histone methyltransferase, as well as histone acet-
ylase inhibitors, may have significant potential.
THE FUTURE OF EPIGENETICS
For many decades, the field of epigenetics has grown
exponentially in part because its many effects on the
epigenome has led to a vast number of biological mani-
festations, involving both natural as well as disease pro-
cesses. However, a significant impediment to progress
in this field has been an outgrowth of the same phe-
nomenon, that is, the vast effects epigenetics has on the
genome has made locus-specific studies of epigenetics
processes somewhat limited. However, recent develop-
ments may overcome this persistent impediment.
Exciting new advances in epigenetic editing may con-
tribute significantly to the long sought-after targeting of
8 1. EPIGENETICS OVERVIEW
epigenetic modifications. The development of the clus-
tered regularly interspaced short palindromic repeats
(CRISPR) and CRISPR-associated protein (Cas)
(CRISPR/Cas) system now enables epigenetics research-
ers to target loci of interest and to determine the modi-
fiers of interest in a locus-specific manner as described
in Chapter 42. This capacity for locus-specific epigenetic
editing may spark a new revolution in epigenetic
research and finally allow us to treat many diseases that
are manifested by epigenetic aberrations with a signifi-
cantly reduced risk to the patient, due to the more tar-
geted approach it manifests.
CONCLUSION
Increased understanding of the underlying chemistry
and enzymatic machinery of epigenetics has served to
drive the field of epigenetics well beyond original
expectations, and advances continue at a rapid pace.
This area of research has also significantly expanded
horizontally in that additional epigenetic processes such
as noncoding RNA, prion changes, and Polycomb
mechanisms have now been established. It is likely that
even more epigenetic processes will be discovered in
the not too distant future. A major driving force in epi-
genetics has been the outstanding development of new
technology that has not only served to stimulate new
discoveries, but has also expanded the field by allowing
for novel discoveries possible through the use of these
new tools. The development of new model organisms
for understanding epigenetic processes has also greatly
stimulated the field of epigenetics. We now know that
epigenetics is not only intricately associated with metab-
olism, but also functions in stem cell behavior, tissue
regeneration, the transfer of information through gen-
erations, neurological memory processes, and even the
aging of organisms among may other biological pro-
cesses. Epigenetics has also played key roles in evolu-
tion and has served as a molecular driver of mutations.
Moreover, the changing environment is currently
I. OVERVIEW
reshaping the evolution of many organisms through
epigenetic processes. Epidemiological factors such as
diet, environmental exposure, the gut microbiome as
well as epigenetic-modifying drugs are also influencing
our daily lives through changes in epigenetics. Diseases
that have been associated with changes in epigenetic
processes range from schizophrenia to cancer, and the
list of these diseases continues to undergo rapid expan-
sion. Fortunately, the field of epigenetic therapy is also
developing rapidly and the hope is that the future will
see many novel treatments for the numerous diseases
that are derived from heritable as well as environmen-
tally induced epigenetic aberrations. Advances in locus-
specific targeting of epigenetics through epigenetic edit-
ing and CRISPR/Cas offers but one example, albeit an
important, exciting and perhaps revolutionizing exam-
ple of changes in the future directions of epigenetic
research.
References
[1] Waddington CH. The epigenotype. Endeavour 1942;1942(1):18 20.
[2] Li Y, Saldanha SN, Tollefsbol TO. Impact of epigenetic dietary
compounds on transgenerational prevention of human diseases.
AAPS J 2014;16:27 36.
[3] Tollefsbol TO, editor. Transgenerational epigenetics: evidence
and debate. Second Edition Academic Press; 2019.
[4] Brink RA, Styles ED, Axtell JD. Paramutation: directed genetic
change. Paramutation occurs in somatic cells and heritably alters
the functional state of a locus. Science 1968;159:161 70.
[5] Cavalli G, Paro R. Epigenetic inheritance of active chromatin
after removal of the main transactivator. Science 1999;286:955 8.
[6] Grewal SI, Klar AJ. Chromosomal inheritance of epigenetic states
in fission yeast during mitosis and meiosis. Cell 1996;86:95 101.
[7] Ghai M, Kader F. A review on epigenetic inheritance of experi-
ences in humans Biochem Genet 2021. Available from: https://
doi.org/10.1007/s10528-021-10155-7. Online ahead of print.
PMID. Available from: 34792705.
[8] Lai SR, Phipps SM, Liu L, Andrews LG, Tollefsbol TO. Epigenetic
control of telomerase and modes of telomere maintenance in
aging and abnormal systems. Front Biosci 2005;10:1779 96.
[9] Fuks F, Burgers WA, Brehm A, Hughes-Davies L, Kouzarides T.
DNA methyltransferase Dnmt1 associates with histone deacety-
lase activity. Nat Genet 2000;24:88 91.
 S E C T I O N I I

Molecular Mechanisms of Epigenetics

2. Mechanisms of DNA methylation and demethylation during mammalian development

3. Molecular mechanisms of histone modifications
4. The epigenetics of non-coding RNA
5. Prions and prion-like phenomena in epigenetic inheritance
6. Higher-order chromatin organization in diseases, from chromosomal position effect to phenotype variegation
7. Polycomb mechanisms and epigenetic control of gene activity
This page intentionally left blank
 C H A P T E R

2
Mechanisms of DNA Methylation and
Demethylation During Mammalian
Development
Zhengzhou Ying1,2 and Taiping Chen1
1
Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center,
Houston, TX, United States 2The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, College of
Laboratory Medicine, Chongqing Medical University, Chongqing, P. R. China

O U T L I N E

Introduction 11 Conclusions 20
DNA Methylation 12 Acknowledgments 21
Maintenance DNA Methylation 12
Glossary 21
De novo DNA Methylation 15
Abbreviations 22
DNA Demethylation 17
Passive DNA Demethylation 17 References 22
Active DNA Demethylation 18

INTRODUCTION inactivation, and transposon silencing, and in various dis-

DNA methylation, the covalent addition of a methyl
group to the fifth position of cytosine (5-methylcytosine,
5mC), is the most common form of DNA modification,
which plays important roles in the regulation of chroma-
tin structure and gene expression. DNA methylation is
present in various organisms across all kingdoms of
eukaryotes. In mammals, DNA methylation mostly occurs
in the context of CpG dinucleotides, with 60%
80% of all
CpGs in the genome being methylated, although non-
CpG (i.e., CpA, CpT, or CpC) methylation is abundant in
specific tissues and cell types, including embryonic stem
cells (ESCs), oocytes, and brain tissue [1,2]. DNA methyla-
tion plays diverse roles in mammalian development, such
as gene expression, genomic imprinting, X-chromosome
eases, including cancer and developmental disorders [3].
5mC is not randomly distributed in the genome. In
general, repetitive DNA sequences, including transpos-
able elements and centromeric and pericentric satellite
DNA, are heavily methylated. In contrast, CpG islands
(CGIs, 1
2 kilobases of CpG-rich regions) present in
gene promoters are usually depleted of DNA methyla-
tion, with some exceptions. For example, CGIs on the
inactive X chromosome in female cells are hyper-
methylated, and CGIs in imprinting control regions
(ICRs) exhibit allele-specific methylation. On the other
hand, gene bodies are often highly methylated. Unlike
promoter methylation, which correlates with gene
silencing, gene body methylation is usually associated
with transcriptional activity [3].

Handbook of Epigenetics.
DOI: https://doi.org/10.1016/B978-0-323-91909-8.00009-8 11 Copyright © 2023 Elsevier Inc. All rights reserved.
12 2. MECHANISMS OF DNA METHYLATION AND DEMETHYLATION DURING MAMMALIAN DEVELOPMENT
DNA methylation patterns and levels are determined
by the opposing actions of the methylation and demethyl-
ation machineries. The methylation machinery includes
DNA methyltransferases (DNMTs), which catalyze the
transfer of a methyl group from the methyl donor S-ade-
nosyl-L-methionine (AdoMet or SAM) to the C-5 position
of cytosines. There are two families of DNMTs in mam-
mals; DNMT1 is mainly responsible for maintaining
DNA methylation patterns through DNA replication,
whereas DNMT3A and DNMT3B function primarily as
de novo methyltransferases that establish DNA methyla-
tion patterns [4]. In rodents, there is an additional de
novo methyltransferase, DNMT3C, which is produced by
a duplicated gene of Dnmt3b and specifically methylates
evolutionarily young transposons during spermatogene-
sis [5]. From a chemical perspective, DNA methylation
is considered a stable modification. However, global
demethylation occurs in preimplantation embryos and
primordial germ cells (PGCs), and locus-specific demeth-
ylation takes place during cellular differentiation. DNA
demethylation can be achieved by replication-dependent
“passive” dilution of 5mC and replication-independent
“active” processes [6,7]. Great progress has been made in
understanding the mechanisms of demethylation since
the discovery that the TET family of proteins—TET1,
TET2, and TET3—function as 5mC dioxygenases that
convert 5mC, sequentially, to 5-hydroxymethylcytosine
(5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine
(5caC) [8
11], which serve as intermediates for DNA
demethylation [6,7].
DNA METHYLATION
In 1975, Holliday, Pugh, and Riggs proposed that DNA
methylation could be important for cellular memory by
serving as a heritable epigenetic mark through cell divi-
sion [12,13]. Based on the complementarity of CpG/CpG
dyads, they reasoned that methylated CpG sites could be
replicated semiconservatively during DNA replication.
The theory would predict the existence of at least two
DNA methylation activities: de novo methylation puts
methyl marks at unmodified CpG/CpG dyads to estab-
lish DNA methylation patterns, and maintenance methyl-
ation converts newly formed hemimethylated CpG sites
during DNA replication into fully methylated state to
maintain the patterns (Fig. 2.1). The hypothesis was subse-
quently validated, to a large extent, by the identification
of DNA methyltransferases with distinct expression pat-
terns, biochemical properties, and biological functions [4].
Maintenance DNA Methylation
Once DNA methylation patterns are established dur-
ing embryogenesis, they are maintained in somatic cells
II. MOLECULAR MECHANISMS OF EPIGENETICS
in a cell type-specific manner. During each round of
DNA replication, DNA becomes hemimethylated, as
only CpGs on the parental strand remain methylated
while CpGs on the newly replicated daughter strand are
unmethylated. To reestablish the symmetry of CpG
methylation and keep the specificity, the maintenance
DNA methyltransferase activity recognizes hemimethy-
lated CpGs and methylates the corresponding CpGs on
the daughter strand. Biochemical, cellular, and genetic
evidence suggests that DNMT1 is the major maintenance
methyltransferase [4]. In addition, a multidomain pro-
tein, UHRF1 (ubiquitin-like with PHD and RING finger
domains 1), functions as an essential accessory factor
that directs DNMT1 to the right place [14,15].
DNMT1
Mouse Dnmt1, the first mammalian DNA methyl-
transferase gene identified [16], has several transcription
start sites and produces two major protein products.
Transcripts initiated within a somatic cell-specific exon
encode the full-length DNMT1 protein that is expressed
in somatic cell types, whereas transcripts initiated within
an oocyte-specific exon utilize a downstream AUG as the
translation initiation codon, resulting in the DNMT1o
isoform that lacks the N-terminal 118 amino acids of full-
length DNMT1 (Fig. 2.2A). Both isoforms are equally
functional in maintaining DNA methylation, although
DNMT1o is more stable than DNMT1 [17].
While all DNMTs contain highly conserved DNA
methyltransferase motifs in their C-terminal catalytic
domains, the DNMT1 and DNMT3 families show little
sequence similarity in their N-terminal regulatory
domains (Fig. 2.2A). There are several unique domains
in the N-terminal region of DNMT1, which likely con-
tribute to functional specificity. A region at the very N
terminus mediates the interaction between DNMT1 and
DNA methyltransferase associated protein 1 (DMAP1),
a protein implicated in histone acetylation and ATM
signaling. The DMAP1-interaction domain is absent in
the more stable DNMT1o isoform [17], suggesting that
this domain or the interaction between DNMT1 and
DMAP1 may be involved in regulating DNMT1 stabil-
ity. The DMAP1-interaction domain is followed by a
proliferating cell nuclear antigen (PCNA) binding
domain (PBD), which is required for the interaction
with the DNA replication machinery, and a nuclear
localization signal (NLS). DNMT1 also contains a motif
originally named as the replication foci-targeting
sequence (RFTS). Subsequent evidence indicates that
RFTS contains a ubiquitin-interacting motif (UIM) that
recognizes ubiquitinated lysines in the N-terminal tail
of histone H3, which likely plays an important role in
targeting DNMT1 to replication foci [18]. Structural
data suggest that the RFTS domain also plays an autoin-
hibitory role in the regulation of DNMT1 activity by
 DNA METHYLATION 13

Unmethylated

De novo
methylation Active demethylation

Methylated

A n
DNA Maintenance D N atio
l i c
replication methylation r ep

Hemimethylated DNA
DNA replication replication

Passive demethylation

FIGURE 2.1 Overview of mechanisms of DNA methylation and demethylation. During early development, de novo methylation adds
methyl groups to specific CpG sites on both DNA strands (resulting in symmetric CpG methylation) and establishes DNA methylation pat-
terns. After each round of DNA replication, the methylated CpG sites become hemimethylated, as the newly replicated daughter DNA strand
is unmethylated. Maintenance methylation recognizes hemimethylated CpG sites and “copies” the DNA methylation pattern of the parental
strand onto the daughter strand. Failure in maintenance methylation results in replication-dependent loss of DNA methylation, a process
known as passive demethylation. DNA demethylation can also be achieved by enzyme-mediated removal of the methyl group or replacement
of methylated cytosines (or their derivatives) with unmodified cytosines, a process known as active demethylation, which is independent of
DNA replication. Open and filled circles indicate unmethylated and methylated CpG dinucleotides, respectively.

binding to the catalytic domain and blocks the catalytic
center [19]. Additionally, DNMT1 contains a CXXC
domain, a cysteine-rich motif that binds unmethylated
CpGs, and a pair of bromo-adjacent homology (BAH)
domains, BAH1 and BAH2. While the precise function
of the BAH domains remains unknown, they are
required for DNMT1 to be associated with the replica-
tion foci during S phase [20].
Biochemical assays reveal that DNMT1 preferentially
methylates hemimethylated CpG dinucleotides, although
it is capable of methylating unmethylated substrates as
well [21]. Dnmt1 is constitutively expressed in proliferat-
ing cells. During S phase, DNMT1 is increased and
associates with the replication foci, suggesting that
DNMT1 function is coupled with DNA replication [22].
Genetic inactivation of Dnmt1 in mouse ESCs results in
global loss of DNA methylation, but does not affect de
novo methylation of integrated provirus DNA [23,24].
These results suggest that DNMT1 functions primarily as
a maintenance methyltransferase. Recent studies suggest
that DNMT1 is also involved in de novo methylation in
specific genomic regions (e.g., retrotransposons) and
such activity is probably inhibited in other contexts
[25,26].
DNA methylation is dispensable in undifferentiated
mouse ESCs, as Dnmt1 knockout (KO), Dnmt3a/3b dou-
ble KO (DKO), and Dnmt1/3a/3b triple KO (TKO) ESCs
show no defects in viability and proliferation, but these
cells die when induced to differentiate [24,27
30].
Unlike mouse ESCs, human ESCs require DNMT1, but
not DNMT3A and DNMT3B, for survival [31]. Mouse
and human ESCs represent different pluripotent states,
with mouse ESCs being more similar to naı̈ve pluripo-
tent cells and human ESCs being in primed pluripotent
state, which may explain the sensitivity of human ESCs
to hypomethylation. DNMT1 is also required for the sur-
vival of mouse embryonic fibroblasts (MEFs) and the
human colorectal cancer cell HCT116 [32,33]. These find-
ings suggest crucial roles for DNMT1 in cellular differen-
tiation and in the viability of differentiated cells. Indeed,
complete inactivation of Dnmt1 results in gastrulation
defects and embryonic lethality [24]. In human, missense
DNMT1 mutations in the RFTS of the N-terminal regula-
tory domain, which likely results in hypomorphic alleles,
have been identified in two related neurodegenerative
disorders, hereditary sensory, and autonomic neuropathy
with dementia and hearing loss type IE (HSAN IE) and
autosomal dominant cerebellar ataxia, deafness, and nar-
colepsy (ADCA-DN) [34].
UHRF1
UHRF1 is a multidomain protein. Genetic studies
demonstrate that UHRF1 is essential for maintaining
DNA methylation. Similar to the phenotype of Dnmt1

II. MOLECULAR MECHANISMS OF EPIGENETICS

14 2. MECHANISMS OF DNA METHYLATION AND DEMETHYLATION DURING MAMMALIAN DEVELOPMENT

(A)
N-terminal regulatory domain C-terminal catalytic domain

PBD
NLS
UIM

GK
DMAP1 CXXC BAH1 BAH2 I IV VII VIII IX X
DNMT1 RFTS 1620

DNMT1o 1502

PWWP ADD I IV VII VIII IX X

DNMT3A1 908

DNMT3A2 689

PWWP ADD I IV VII VIII IX X

DNMT3B1 859

DNMT3B2 839

DNMT3B3 776
∆63

DNMT3B4 730

DNMT3B5 798

DNMT3B6 796
∆63

ADD I IV VII VIII

DNMT3L 421
∆63

(B)
UBL TDD PHD SRA RING
UHRF1 782

FIGURE 2.2 Schematic diagram of major proteins involved in DNA methylation. (A) Major DNMT isoforms in mouse. The DNMT1 and
DNMT3 families of proteins share conserved catalytic motifs (I
X) in their C-terminal catalytic domains. DNMT3L lacks catalytic activity
because some essential motifs are missing or mutated. The N-terminal regions of DNMT1 and DNMT3 proteins have little sequence similarity,
with distinct domains that contribute to their functional specificities. DMAP1, DNA methyltransferase associated protein 1; PBD, PCNA-
binding domain; NLS, nuclear localization signal; RFTS, replication foci targeting sequence; UIM, ubiquitin interacting motif; CXXC, cysteine-
rich motif; BAH, bromo-adjacent homology; GK, glycine/lysine repeats; I
X, DNA methyltransferase conserved catalytic motifs; PWWP, pro-
line-tryptophan-tryptophan-proline; ADD, ATRX-DNMT3-DNMT3L. Note that DNMT3B3 and DNMT3B6 have the exact
63-residue deletion corresponding to that of DNMT3L. (B) Mouse UHRF1. UBL, ubiquitin-like domain; TTD, tandem tudor domain; PHD,
plant homeodomain; SRA, SET and RING associated; RING, really interesting new gene.

deficiency, disruption of Uhrf1 leads to embryonic
lethality and global DNA hypomethylation [14,15,35].
Cellular studies also suggest functional interactions
between DNMT1 and UHRF1. Both proteins are
enriched at DNA replication foci during the S phase,
but DNMT1 fails to localize to these foci in Uhrf1 KO
cells [14,15]. These findings indicate that UHRF1 is a
critical regulator of maintenance methylation by direct-
ing DNMT1 to hemimethylated CpG sites.
UHRF1 has five conserved domains: a ubiquitin-like
(UBL) domain, a tandem tudor domain (TTD), a plant
homeodomain (PHD), a Really Interesting New Gene
(RING) domain, and a SET and RING associated (SRA)
domain (Fig. 2.2B). The SRA domain preferentially binds
hemimethylated DNA and likely plays an important role
in loading DNMT1 onto newly synthesized DNA sub-
strates [14,15]. The TTD and PHD act in combination to
recognize the histone H3 trimethylated at lysine
9 (H3K9me3) mark, and additionally, the PHD binds to
histone H3 with unmethylated arginine 2 (H3R2me0)
[36,37]. The RING finger domain has E3 ubiquitin ligase
activity, and the UBL domain facilitates ubiquitination
by stabilizing the E2-E3-chromatin complex [38,39].
UHRF1 has been shown to catalyze monoubiquitination
of histone H3 at several lysine residues (K14/K18/K23)
in the N-terminal tail, creating DNMT1-binding sites
[18,40,41]. Thus, UHRF1 directs DNMT1 to hemimethy-
lated CpG sites through multivalent interactions with

II. MOLECULAR MECHANISMS OF EPIGENETICS

 DNA METHYLATION
chromatin to ensure faithful inheritance of DNA methyl-
ation patterns during and/or after DNA replication.
De novo DNA Methylation
After fertilization, both the maternal and paternal gen-
omes undergo global DNA demethylation during preim-
plantation development. As a result, DNA methylation
marks inherited from gametes are largely erased by the
blastocyst stage, with the exception of those in ICRs of
imprinted loci and some retrotransposons. After implanta-
tion, a wave of de novo methylation occurs in the epiblast
to establish the initial pattern of DNA methylation. DNA
methylation shows further changes during cellular differ-
entiation, and the patterns are then stably maintained in a
lineage-specific manner. Similar epigenetic reprograming
events also take place during gametogenesis, including
global demethylation in PGCs. Subsequently, a new
round of de novo DNA methylation takes place during
gametogenesis, resulting in different methylation patterns
in male and female gametes [3]. De novo methylation
is mediated by DNMT3A and DNMT3B (in rodents,
DNMT3C also participates in de novo methylation during
spermatogenesis). Another member of the DNMT3 family,
DNMT3-like (DNMT3L), has no catalytic activity but is an
important regulator of de novo methylation (Fig. 2.2A).
DNMT3A and DNMT3B
The Dnmt3a and Dnmt3b genes were initially identi-
fied by searching an expressed sequence tag (EST)
database using bacterial type II cytosine-5 methyltrans-
ferase sequences as queries. Their protein products
have a similar structural organization, including a
C-terminal catalytic domain that contains sequence
motifs characteristic of all DNA methyltransferases
and an N-terminal regulatory domain that is distinct
from that of DNMT1 (Fig. 2.2A) [42]. The N-terminal
regions of DNMT3A/3B contain two conserved
domains implicated in chromatin binding. The proline-
tryptophan-tryptophan-proline (PWWP) domain, an
B150-residue domain with a conserved PWWP motif,
is necessary for targeting the enzymes to heterochro-
matin, intergenic and genic regions and mediates bind-
ing to H3K36me2 and H3K36me3 marks [43
46]. The
ADD (ATRX-DNMT3-DNMT3L) domain interacts with
the N-terminal tail of histone H3 with unmodified
lysine 4 (H3K4me0) [47,48]. Structural studies revealed
that the ADD domain of DNMT3A interacts with its
catalytic domain and blocks its DNA-binding affinity,
resulting in autoinhibition. Unmodified histone H3 tail
(but not H3 tail with H3K4me3) can disrupt the inter-
action between the ADD and the catalytic domains,
leading to DNMT3A activation [49]. DNMT3A/3B also
have distinct unstructured regions at the very N
II. MOLECULAR MECHANISMS OF EPIGENETICS
15
termini. Recent work suggests that the unstructured
region of DNMT3A is functionally important [50] and
interacts with H2AK119ub-modified nucleosomes [51].
These findings indicate that DNMT3A and DNMT3B
act as both “writers” and “readers” of epigenetic
marks and that their activities and specificities are reg-
ulated by specific histone modifications.
The conclusion that DNMT3A and DNMT3B func-
tion primarily as de novo methyltransferases is based
on several lines of evidence. First, Dnmt3a and Dnmt3b
expression correlates with de novo methylation during
development. Specifically, Dnmt3a and Dnmt3b are
highly expressed in early embryos (as well as ESCs)
and developing germ cells, and their expression is sig-
nificantly downregulated in somatic cells and when
ESCs are differentiated [42]. In ESCs and germ cells,
Dnmt3a transcription is mostly driven by an internal
promoter, resulting in a shorter isoform known as
DNMT3A2, which lacks the N-terminal 219 (mouse) or
223 (human) amino acids of full-length DNMT3A1
(Fig. 2.2A). DNMT3A1 is ubiquitously expressed at low
levels in most somatic tissues [52]. Dnmt3b produces mul-
tiple alternatively spliced isoforms ( . 30 reported to
date), many of which are catalytically inactive (Fig. 2.2A).
In ESCs and early embryos, the full-length isoform
DNMT3B1, a catalytically active form, is the predominant
product, and other isoforms, including the inactive
DNMT3B6, are also expressed. In most somatic cells,
Dnmt3b expression is low, usually with both active (e.g.,
DNMT3B2) and inactive (e.g., DNMT3B3) isoforms
[42,52]. Recent work suggests that the inactive DNMT3B3
and DNMT3B6 isoforms, which, like DNMT3L, lack
63 amino acids in their catalytic domains (Fig. 2.2A), posi-
tively regulate de novo methylation by DNMT3A/3B
with a preference for DNMT3B [50].
Second, biochemical studies indicate that DNMT3A
and DNMT3B behave as de novo methyltransferases. In
particular, recombinant DNMT3A/3B proteins show no
preference for hemimethylated DNA over unmethylated
DNA in vitro, unlike DNMT1, which preferentially
methylates hemimethylated DNA [21,42]. Furthermore,
in vitro and in vivo evidence indicates that DNMT3A
and DNMT3B methylate cytosines at non-CpG sites, such
as CpA and CpT, albeit with lower efficiency compared
to CpG methylation [53]. Non-CpG methylation, which
cannot be maintained during DNA replication, is medi-
ated by de novo methyltransferases.
Third, genetic studies provide definitive evidence
for the involvement of DNMT3A and DNMT3B in de
novo DNA methylation. Targeted disruption of both
Dnmt3a and Dnmt3b blocks de novo methylation in
mouse ESCs and early embryos but has no effect on
the maintenance of methylation at imprinted loci
[28,54]. While DNMT3A and DNMT3B methylate
many genomic loci redundantly, they also have
Another random document with
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The Project Gutenberg eBook of Gay-Neck
 This ebook is for the use of anyone anywhere in the United
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eBook.

Title: Gay-Neck
The story of a pigeon

Author: Dhan Gopal Mukerji

Illustrator: Boris Artzybasheff

Release date: November 10, 2023 [eBook #72086]

Language: English

Original publication: New York, NY: E.P. Dutton & Co., Inc, 1927

Credits: Greg Weeks, Mary Meehan and the Online Distributed

Proofreading Team at http://www.pgdp.net

*** START OF THE PROJECT GUTENBERG EBOOK GAY-NECK ***

Gay-Neck
 Copyright, 1927
By E. P. DUTTON & COMPANY

All rights reserved

First Printing July, 1927
Fifth Printing Dec., 1927
Tenth Printing May, 1928
Fifteenth Printing Oct., 1928
Seventeenth Printing Jan., 1929
 Eighteenth Printing June, 1929
Nineteenth Printing Nov., 1929
Twentieth Printing Nov., 1929

Printed in the United States of America

This book was awarded the

John Newbery Medal by the
Children's Librarians' Section of
the American Library
Association, for the most
distinguished contribution to
American Children's literature
during the year 1927.

By the same author

CASTE AND OUTCAST

MY BROTHER'S FACE
THE SECRET LISTENERS OF THE EAST
THE FACE OF SILENCE
 Stories for Children

KARI THE ELEPHANT

JUNGLE BEASTS AND MEN
HARI THE JUNGLE LAD
GAY-NECK (The Story of a Pigeon)

Published by
E. P. DUTTON & CO., INC.
 TO

Dear Suresh:
Since Gay-Neck needs a protector I thought of you for several
reasons. First of all being a poet, an observer of nature, and a
traveller, you would be able to protect the book from being
condemned. In fact, there is no one who can do it as well as yourself.
You know the country where Gay-Neck grew. You are versed in the
lore of birds. For a pigeon, life is a repetition of two incidents: namely,
quest of food and avoidance of attacks by its enemies. If the hero of
the present book repeats his escapes from attacks by hawks, it is
because that is the sort of mishap that becomes chronic in the case
of pigeons.
Now as to my sources, you well know that they are too numerous to
be mentioned here. Many hunters, poets like yourself, and books in
many languages have helped me to write Gay-Neck. And if you will
permit it, I hope to discharge at least a part of my debt by dedicating
this book to one of my sources—yourself.
I remain most faithfully yours,
Dhan Gopal.
 CONTENTS
PART I
I. Birth of Gay-Neck
II Education of Gay-Neck
III. Training in Direction
IV. Gay-Neck in the Himalayas
V. On Gay-Neck's Track
VI. Gay-Neck's Truancy
VII. Gay-Neck's Story
VIII. Gay-Neck's Odyssey (Continued)

PART II
I. Gay-Neck's Training for War
II. War Training (Continued)
III. Mating of Gay-Neck
IV. War Calls Gay-Neck
V. Second Adventure
VI. Ghond Goes Reconnoitring
VII. Gay-Neck Tells How He Carried the Message
VIII. Healing of Hate and Fear
IX. The Wisdom of the Lama
 LIST OF ILLUSTRATIONS
Gay-Neck
With Enormously Long Reach He almost Touched the Top of
the Tree
No Beast of Prey Can Kill His Victim without Frightening Him
First
That Sound was Drowned in the Cry of the Eagles above
Who Screeched Like Mad, Slaying Each Other
GAY-NECK
PART I
CHAPTER I
 BIRTH OF GAY-NECK
he city of Calcutta, which boasts of a million
people, must have at least two million pigeons.
Every third Hindu boy has perhaps a dozen pet
carriers, tumblers, fantails, and pouters. The art of
domesticating pigeons goes back thousands of
years in India, and she has contributed two species
of pigeons as a special product of her bird fanciers,
the fantail and the pouter. Love and care have
been showered on pigeons for centuries by emperors, princes and
queens in their marble palaces, as well as by the poor, in their
humble homes. The gardens, grottos and fountains of the Indian rich
—the small field of flowers and fruits of the common folks, each has
its ornament and music,—many-colored pigeons and cooing white
doves with ruby eyes.
Even now any winter morning foreigners who visit our big cities may
see on the flat-roofed houses innumerable boys waving white flags
as signals to their pet pigeons flying up in the crisp cold air. Through
the blue heavens flocks of the birds soar like vast clouds. They start
in small flocks and spend about twenty minutes circling over the
roofs of their owners' homes. Then they slowly ascend and all the
separate groups from different houses of the town merge into one
big flock and float far out of sight. How they ever return to their own
homes is a wonder, for all the house-tops look alike in shape in spite
of their rose, yellow, violet and white colors.
But pigeons have an amazing sense of direction and love of their
owners. I have yet to see creatures more loyal than pigeons and
elephants. I have played with both, and the tusker on four feet in the
country, or the bird on two wings in the city, no matter how far they
wandered, were by their almost infallible instinct brought back to
their friend and brother—Man.
My elephant friend was called Kari, of whom you have heard before,
and the other pet that I knew well was a pigeon. His name was
Chitra-griva; Chitra meaning painted in gay colours, and Griva, neck
—in one phrase, pigeon Gay-Neck. Sometimes he was called
"Iridescence-throated."
Of course Gay-Neck did not come out of his egg with an iridescent
throat; he had to grow the feathers week by week; and until he was
three months old, there was very little hope that he would acquire the
brilliant collar, but at last when he did achieve it, he was the most
beautiful pigeon in my town in India, and the boys of my town owned
forty thousand pigeons.
But I must begin this story at the very beginning, I mean with Gay-
Neck's parents. His father was a tumbler who married the most
beautiful pigeon of his day; she came from a noble old stock of
carriers. That is why Gay-Neck proved himself later such a worthy
carrier pigeon in war as well as in peace. From his mother he
inherited wisdom, from his father bravery and alertness. He was so
quick-witted that sometimes he escaped the clutches of a hawk by
tumbling at the last moment right over the enemy's head. But of that
later, in its proper time and place.
Now let me tell you what a narrow escape Gay-Neck had while still in
the egg. I shall never forget the day when, through a mistake of
mine, I broke one of the two eggs that his mother had laid. It was
very stupid of me. I regret it even now. Who knows, maybe with that
broken egg perished the finest pigeon of the world. It happened in
this way. Our house was four stories high—and on its roof was built
our pigeon house. A few days after the eggs were laid I decided to
clean the pigeon hole in which Gay-Neck's mother was sitting on
them. I lifted her gently and put her on the roof beside me. Then I
lifted each egg carefully and put it most softly in the next pigeon
hole; which however had no cotton nor flannel on its hard wooden
floor. Then I busied myself with the task of removing the debris from
the birth-nest. As soon as that was done, I brought one egg back
and restored it to its proper place. Next I reached for the second one
and laid a gentle but firm hand on it. Just then something fell upon
my face like a roof blown by the storm. It was Gay-Neck's father
furiously beating my face with his wings. Worse still, he had placed
the claws of one of his feet on my nose. The pain and surprise of it
was so great that ere I knew how, I had dropped the egg. I was
engrossed in beating off the bird from my head and face and at last
he flew away. But too late; the little egg lay broken in a mess at my
feet. I was furious with its clumsy father and also with myself. Why
with myself? Because I should have been prepared for the father
bird's attack. He took me for a stealer of his eggs, and in his
ignorance was risking his life to prevent my robbing his nest. May I
impress it upon you that you should anticipate all kinds of surprise
attacks when cleaning a bird's home during nesting season.
But to go on with our story. The mother bird knew the day when she
was to break open the egg-shell with her own beak, in order to usher
Gay-Neck into the world. Though the male sits on the egg pretty
nearly one third of the time—for he does that each day from morning
till late afternoon—yet he does not know when the hour of his child's
birth is at hand. No one save the mother bird arrives at that divine
certainty. We do not yet understand the nature of the unique wireless
message by which she learns that within the shell the yolk and the
white of her egg have turned into a baby-bird. She also knows how
to tap the right spot so that the shell will break open without injuring
her child in the slightest. To me that is as good as a miracle.
Gay-Neck's birth happened exactly as I have described. About the
twentieth day after the laying of the egg I noticed that the mother
was not sitting on it any more. She pecked the father and drove him
away every time he flew down from the roof of the house and
volunteered to sit on the egg. Then he cooed, which meant, "Why do
you send me away?"
She, the mother, just pecked him the more, meaning, "Please go.
The business on hand is very serious."
At that, the father flew away. That worried me, for I was anxious for
the egg to hatch, and was feeling suspicious about its doing it at all.
With increased interest and anxiety I watched the pigeon hole. An
hour passed. Nothing happened. It was about the third quarter of the
next hour that the mother turned her head one way and listened to
something—probably a stirring inside that egg. Then she gave a
slight start. I felt as if a tremor were running through her whole body.
With it a great resolution came into her. Now she raised her head,
and took aim. In two strokes she cracked the egg open, revealing a
wee bird, all beak and a tiny shivering body! Now watch the mother.
She is surprised. Was it this that she was expecting all these long
days? Oh, how small, how helpless! The moment she realizes her
child's helplessness, she covers him up with the soft blue feathers of
her breast.
CHAPTER II