DNA Methyltransferases - Role and Function

Preface
Contents
About the Editors
1: Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges
	1.1 Discovery of DNA Methylation
	1.2 Discovery and Early Work on DNA MTases
	1.3 DNA MTases Contain Conserved Amino Acids Sequence Motifs
	1.4 Structure and Mechanism of DNA MTases
	1.5 Molecular Evolution of MTases
	1.6 Early Views on the Biological Role of DNA Methylation
	1.7 Genetic Studies on DNMTs in Mammals
	1.8 Structure, Function, and Regulation of Mammalian DNA MTases
	1.9 Discovery of TET Enzymes
	1.10 Methods for Site-Specific Detection of DNA Methylation
	1.11 DNA MTases and Bacterial Epigenetics
	1.12 Role of DNA Methylation in Cancer
	1.13 Application of MTases in Artificial Epigenetic Systems
	1.14 Conclusions and Outlook
	References
2: DNA Methylation in Prokaryotes
	2.1 Introduction
	2.2 CcrM Methylation
	2.3 Dam Methylation
		2.3.1 Role of Dam Methylation in DNA Mismatch Repair
		2.3.2 Control of Chromosome Replication by Dam Methylation
		2.3.3 Transcriptional Control by Dam Methylation
			2.3.3.1 Temporal Regulation of Gene Expression by Dam Methylation
			2.3.3.2 Regulation of Bistability by Dam Methylation
	2.4 Phase Variable DNA Adenine Methylation
	2.5 Additional Examples of DNA Adenine Methylation
	2.6 C5-Methylcytosine
	2.7 N4-Methylcytosine
	2.8 Biomedical and Biotechnological Applications of Dam Methylation
	References
3: Domain Structure of the Dnmt1, Dnmt3a, and Dnmt3b DNA Methyltransferases
	3.1 DNA Methylation and Methyltransferases in Mammals
	3.2 Enzymes Responsible for the Establishment of DNA Methylation Patterns
		3.2.1 PWWP Domain
		3.2.2 ADD Domain
		3.2.3 Catalytic Domain
		3.2.4 Functions of Other Regions
		3.2.5 Factors That Guide Dnmt3 to the Regions to Be Methylated
		3.2.6 Correlation Between de novo DNA Methylation and Histone Modifications
	3.3 Enzymes Responsible for the Maintenance of DNA Methylation Patterns
		3.3.1 NTD
		3.3.2 RFTS Domain
		3.3.3 CXXC
		3.3.4 Two BAH Domains
		3.3.5 Catalytic Domain
	3.4 Cross-Talk Between De Novo-Type and Maintenance-Type DNA Methyltransferases
	3.5 Conclusions and Perspective
	References
4: Enzymology of Mammalian DNA Methyltransferases
	4.1 Introduction
	4.2 General Features of Mammalian DNMTs
		4.2.1 Structure and Domain Composition of Mammalian DNMTs
		4.2.2 Catalytic Mechanism of C5-MTases
		4.2.3 Regulation and Targeting of DNMTs
	4.3 Structure, Function, and Mechanism of DNMT1
		4.3.1 Domain Composition of DNMT1
		4.3.2 Structures of DNMT1 and Allosteric Regulation
		4.3.3 Specificity of DNMT1
		4.3.4 Processivity of DNMT1
		4.3.5 Allosteric Regulation and Targeting of DNMT1
			4.3.5.1 The DNMT1-PCNA Interaction
			4.3.5.2 The DNMT1-UHRF1 Interaction
			4.3.5.3 Binding of the DNMT1-RFTD to Ubiquitinated H3 Tails
			4.3.5.4 Binding of DNMT1 to Heterochromatic Chromatin Marks
			4.3.5.5 Regulation of Activity and Specificity of DNMT1 by Nucleic Acid Binding
		4.3.6 PTMs of DNMT1
			4.3.6.1 Phosphorylation of DNMT1
			4.3.6.2 Acetylation and Ubiquitination of DNMT1
			4.3.6.3 Lysine Methylation of DNMT1
	4.4 Structure, Function, and Mechanism of DNMT3 Enzymes
		4.4.1 Domain Composition of DNMT3 Proteins
		4.4.2 Structures of DNMT3A and DNMT3B
		4.4.3 Allosteric Regulation of DNMT3A
		4.4.4 Specificity of DNMT3 Enzymes
		4.4.5 Kinetic Mechanism of DNMT3 Enzymes
		4.4.6 Oligomerization of DNMT3 Enzymes
			4.4.6.1 Protein Multimerization of DNMT3 Enzymes
			4.4.6.2 Multimerization of DNMT3A and DNMT3A/DNMT3L on DNA
		4.4.7 Direct Chromatin Interaction of DNMT3 Enzymes
			4.4.7.1 Binding of the DNMT3 ADD Domain to H3 Tails
			4.4.7.2 Binding of DNMT3 PWWP Domain to H3 Methylated at K36
			4.4.7.3 H2AK119ub Binding of DNMT3A1
		4.4.8 Interaction Partners of DNMT3s
			4.4.8.1 DNMT3A/DNMT3L Interaction
			4.4.8.2 Interaction of DNMT3A with MeCP2
			4.4.8.3 Other DNMT3A Interacting Proteins
		4.4.9 Phosphorylation of DNMT3A
		4.4.10 Binding of Regulatory DNA and RNA to DNMT3 Enzymes
	4.5 Outlook
	References
5: Genetic Studies on Mammalian DNA Methyltransferases
	5.1 Distinct Roles of Dnmt1 and Dnmt3 Families in DNA Methylation
		5.1.1 Dnmt1: The Maintenance DNA Methyltransferase
		5.1.2 Dnmt3 Family: Key Components of De Novo Methylation Machinery
		5.1.3 Uhrf1: A Major Regulator of Maintenance DNA Methylation
	5.2 Dnmts in Embryonic Development and Cellular Differentiation
		5.2.1 Roles of Dnmts in Embryonic Development
		5.2.2 Roles of Dnmts in Cellular Differentiation and Maintenance of Cell Identity.
		5.2.3 DNMT Mutations in Human Diseases
	5.3 Dnmts in Genomic Imprinting
		5.3.1 Establishment of DNA Methylation Imprints during Gametogenesis
		5.3.2 Maintenance of DNA Methylation Imprints during Development
		5.3.3 Erasure of DNA Methylation Imprints in Primordial Germ Cells
		5.3.4 Noncanonical Genomic Imprinting
	5.4 Concluding Remarks
	References
6: Structure and Mechanism of Plant DNA Methyltransferases
	6.1 Introduction
	6.2 Structure and Mechanism of Plant DNA MTases
		6.2.1 Structural Mechanism of the Maintenance of CHG Methylation in Plants
			6.2.1.1 Overview of Plant CHG DNA Methylation
			6.2.1.2 Structure and Mechanism of CMT3
			6.2.1.3 Structure and Mechanism of KRYPTONITE
		6.2.2 Mechanism of CMT2-Mediated CHH Methylation
		6.2.3 RNA-Directed DNA Methylation (RdDM)
			6.2.3.1 Overview of RdDM
			6.2.3.2 Structure and Mechanism of DRM2
		6.2.4 Potential Mechanism of MET1 in CG Methylation Maintenance
	6.3 Conclusion and Perspective
	References
7: DNA Methylation in Honey Bees and the Unresolved Questions in Insect Methylomics
	7.1 Introduction
	7.2 Genotype to Phenotype
	7.3 The Epigenetic Control of Gene Expression
	7.4 DNA Methylation
		7.4.1 Conserved and Non-Conserved Features of DNA Methylation Enzymology in Animals
		7.4.2 DNMTs and Establishing DNA Methylation Patterns in the Honey Bee
		7.4.3 How do TET Enzymes Contribute to Gene Regulation in the Honey Bees and Other Insects?
		7.4.4 DNA Methylation Patterns Across Invertebrates
		7.4.5 Does Gene Body Methylation Direct Gene Expression in Insects?
	7.5 Conclusion
	References
8: N6-methyladenine: A Rare and Dynamic DNA Mark
	8.1 Introduction
	8.2 Types of DNA Modifications
	8.3 Discovery of 6mA in Various Eukaryotes
	8.4 Abundance of 6mA
	8.5 Methods of Detecting 6mA
	8.6 6mA Regulating Enzymes
		8.6.1 DNA Methyltransferases
		8.6.2 Mechanism of 6mA Methyltransferases
	8.7 DNA Adenine Demethylation
	8.8 6mA Binding Proteins
	8.9 Biological Functions of 6mA
		8.9.1 Effects of Adenine Methylation on DNA Structure
		8.9.2 Restriction-Modification Systems
		8.9.3 DNA Damage Control
		8.9.4 Effect on Transcription
		8.9.5 Nucleosome Positioning
		8.9.6 Cell Cycle Regulation
		8.9.7 Transgenerational Inheritance
	8.10 Conclusions and Future Directions
	References
9: Pathways of DNA Demethylation
	9.1 DNA Methylation: One Building Block of the Epigenome
	9.2 DNA Methylation Reprogramming: Setting the Epigenome Up for Success
	9.3 Active DNA Demethylation: The Hunt for the `Demethylase´
	9.4 Direct DNA Demethylation
	9.5 Indirect Loss of DNA Methylation
		9.5.1 Role of Cytosine Deamination in DNA Demethylation
		9.5.2 Methylcytosine Oxidation-Based Demethylation Mechanisms
	9.6 Chromatin Remodelling, DNA Replication, and Repair: The Epigenetic Triumvirate
	9.7 Replication-Coupled Loss of DNA Methylation: Passive Demethylation
	9.8 Resetting and Erasure of the Germline: A Barrier Against Transgenerational Inheritance
		9.8.1 Demethylation During Preimplantation Development
	9.9 Removing the Molecular Escapement Mechanism to Cell Fate and Aging by Modulation of DNA Methylation: How Cells Can Turn Ba...
	References
10: Structure and Function of TET Enzymes
	10.1 Introduction
	10.2 Discovery of TET-Mediated 5mC Oxidation
		10.2.1 TET-Mediated Iterative Oxidation of 5mC
		10.2.2 TET-Dependent DNA Demethylation
		10.2.3 Mechanisms and Processivity for TET-Mediated Oxidation Reaction
		10.2.4 Oxidation of 5mrC-RNA and 6mA-DNA
	10.3 Function of TET Enzymes
		10.3.1 Distribution of TET Enzymes and 5mC Oxidation Derivatives
		10.3.2 TET in ESCs and Cell Differentiation
		10.3.3 TETs Mediate Epigenetic Reprogramming in Early Embryogenesis and PGC Development
		10.3.4 TET Enzymes in Somatic Cell Reprogramming
		10.3.5 TET Enzymes and Cancer
		10.3.6 TET Enzymes in Neural System
	10.4 Structure of TET Enzymes
		10.4.1 Domain Structure of Human TET Enzymes
		10.4.2 Crystal Structure of the TET2-5mC-DNA Complex
		10.4.3 Crystal Structure of the NgTet1-5mC-DNA Complex
		10.4.4 Structural Basis for Substrate Preference in TET-Mediated Oxidation
		10.4.5 Crystal Structure of Algal TET Homologue CMD1 in Complex with VC and 5mC-DNA
	10.5 Regulation of TET Enzymes
		10.5.1 Inhibitors
		10.5.2 Activators
		10.5.3 Interacting Proteins
	10.6 Concluding Remarks
	References
11: Proteins That Read DNA Methylation
	11.1 Introduction
	11.2 The Methyl-CpG-Binding Domain Family
		11.2.1 MeCP2
		11.2.2 MBD1
		11.2.3 MBD2
		11.2.4 MBD3
		11.2.5 MBD4
		11.2.6 MBD5 and MBD6
	11.3 SET- and RING-Associated (SRA) Domain
		11.3.1 UHRF1
		11.3.2 UHRF2
	11.4 Transcription Factors
		11.4.1 Kaiso and ZBTB38
		11.4.2 CTCF
		11.4.3 ZFP57
		11.4.4 KLF4
		11.4.5 EGR1 and WT1
		11.4.6 bZIP
		11.4.7 Homeodomain Proteins
	11.5 Conclusion
	References
12: Recent Advances on DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications
	12.1 Introduction
	12.2 Base Flipping for Methylation of DNA Bases
		12.2.1 Bacterial DNMTs (HhaI, TaqI, Dam, CcrM, and CamA)
		12.2.2 Mammalian DNMTs (DNMT1, DNMT3A/3L)
		12.2.3 Implications of DNA Methyltransferase Oligomers (DNMT3A/3L, DNMT3A/3B3, EcoP15I, CcrM, and MettL3-14)
		12.2.4 Plant DNMTs
	12.3 Base Flipping in Oxidative Modifications of Methylated Bases
		12.3.1 Eukaryotic TET Enzymes
		12.3.2 AlkB and Homologs
	12.4 Base Flipping in the Recognition of Modified Bases
		12.4.1 Eukaryotic SRA Domains
		12.4.2 EcMcrB-N Homologs as 5mC and N6mA Readers
		12.4.3 5mC and N6mA Readers Use Non-Base-Flipping Recognition
	12.5 Base Flipping in Removing Modified and Unmodified Bases
		12.5.1 Mammalian Thymine DNA Glycosylase (TDG)
		12.5.2 Plant ROS1
		12.5.3 Archaeon PabI Activity as Adenine DNA Glycosylase
	12.6 Conclusions
	References
13: The Role of DNA Methylation and DNA Methyltransferases in Cancer
	13.1 Overview of Genetic and Epigenetic Alterations in Human Cancers
	13.2 DNA Methyltransferases
	13.3 Interplay Between DNA Methyltransferases and Histone Modifiers
	13.4 CpG Islands
	13.5 DNA Methylation
		13.5.1 Tissue-Specific DNA Methylation
		13.5.2 DNA Methylation as a Function of Aging
	13.6 Mutations of Epigenetic Modifier Genes in Human Cancers
	13.7 DNA Hypermethylation in Human Cancers
		13.7.1 Tumor Stratification and DNA Methylation Marker Discovery Accelerated by International Consortia
		13.7.2 Promoter DNA Hypermethylation
		13.7.3 CpG Island Methylator Phenotypes (CIMPs) Stratify Tumor Subclasses
		13.7.4 DNA Hypermethylation of Noncoding RNAs
		13.7.5 DNA Hypomethylation
			13.7.5.1 Repetitive Element DNA Hypomethylation
			13.7.5.2 Partially Methylated Domains (PMDs)
		13.7.6 Whole Genome Bisulfite Sequencing (WGBS) of Cancer Genomes
		13.7.7 Gene Body DNA Methylation
		13.7.8 Enhancer DNA Methylation
	13.8 Liquid Biopsy Measurements of Cancer-Specific DNA Methylation
	13.9 DNA Methylation as a Therapeutic Target
	13.10 Concluding Remarks
	References
14: DNA Methyltransferases and DNA Damage
	14.1 Brief Summary of DNA Methyltransferases
	14.2 DNA Methylation and Regulation of DNA Repair
		14.2.1 Adenine Methylation and DNA Repair in Bacteria
		14.2.2 DNA Methylation and Recombination
	14.3 Direct Effects of DNA Methylation on DNA Damage
		14.3.1 Effect of DNA Methylation of Mutation Rate via Cytosine Deamination
		14.3.2 DNA Alkylation Damage Induction
		14.3.3 DNA Demethylation and DNA Damage
	14.4 Conclusion
	References
15: Role of DNMTs in the Brain
	15.1 Introduction
	15.2 The Mammalian Brain
		15.2.1 Developmental Principles of the Cerebral Cortex as the Seat of Higher Cognitive Functions
	15.3 DNMT Expression in the Brain
	15.4 DNMT Function in the Developing Brain: Neurogenesis
	15.5 DNMT Function in the Developing Brain: Post-mitotic Neuronal Maturation
	15.6 Role of DNMTs in Brain Function, Learning, and Memory
		15.6.1 Functional Implications of DNMTs in Learning and Memory
		15.6.2 DNMTs as Potential Mediators of Cell-Intrinsic Mechanisms for Memory Consolidation and Maintenance
	15.7 DNMTs in Neurodevelopmental and Neuropsychiatric Diseases
	15.8 DNMTs in Neuronal Aging
	15.9 DNMTs in Neurodegeneration
		15.9.1 Alzheimer´s Disease and Tauopathies
		15.9.2 Huntington´s Disease
	15.10 Role of DNMTs in Brain Cancer
		15.10.1 Promoter Methylation
		15.10.2 Methylation of Distal Regulatory Elements
		15.10.3 Implications of Altered DNMT Expression and Targeting in Brain Cancer and Therapy Resistance
		15.10.4 Crosstalk of DNMTs and miRNA-Mediated Translational Control
	15.11 Conclusions
	References
16: Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns
	16.1 Introduction
		16.1.1 DNA Methylation
	16.2 Principles of DNA Methylation Detection
	16.3 Global Methylation Content of a Sample
	16.4 Whole Methylome Analyses
	16.5 Genome-Wide Methylation Analyses Using NGS
		16.5.1 Bisulfite-Based Methods
		16.5.2 Affinity and Antibody-Based Enrichment Methods
		16.5.3 Sequencing Approaches Using Methylation-Sensitive/Dependent Restriction Enzymes
		16.5.4 Epigenotyping Arrays
	16.6 Locus-Specific DNA Methylation Analysis
		16.6.1 Amplicon Bisulfite Sequencing
		16.6.2 Pyrosequencing
		16.6.3 MALDI Mass Spectrometry
		16.6.4 Methylation-Specific PCR and Its Quantitative Variations
	16.7 DNA Methylation Analysis of Circulating Cell-Free DNA
	16.8 Single-Cell DNA Methylation Analysis
	16.9 Analysis of Cytosine Hydroxymethylation
	16.10 Direct Readout of DNA Methylation
	16.11 Combined Analysis of DNA Methylation and Other Epigenetic Modifications
		16.11.1 Histone Modifications
		16.11.2 Nucleosome Positioning
	16.12 Conclusions
	References
17: Inhibitors of DNA Methylation
	17.1 How to Inhibit DNA Methyltransferases
	17.2 Chemistry and Structure of DNMT Inhibitors
	17.3 Potential Applications of DNMT Inhibitors
		17.3.1 DNMTi Application in Cancers
			17.3.1.1 Nucleoside Analogs
				As Single Agent
				Pro-drugs of Nucleoside Analogs
				Nucleoside DNMTi in Combination with Other Drugs
					With Other Epidrugs
					With ``Classical´´ Chemo- and Immunotherapies
			17.3.1.2 Non-nucleoside DNMTi
		17.3.2 DNMTi Application in Neurological and Psychiatric Disorders
			17.3.2.1 Memory Formation
			17.3.2.2 Schizophrenia
			17.3.2.3 Bipolar Disorders
			17.3.2.4 Epilepsy
			17.3.2.5 Post-traumatic Stress Disorder
			17.3.2.6 Depression
			17.3.2.7 X-Chromosome-Related Diseases and Autism Disorders
			17.3.2.8 Parkinson´s and Alzheimer´s Diseases
			17.3.2.9 Aging-Related Senescence and Amyotrophic Lateral Sclerosis
			17.3.2.10 Neuronal Stem Cell
		17.3.3 DNMTi Application in Cardiovascular Diseases
		17.3.4 DNMTi Application in Other Human Pathologies
			17.3.4.1 Obesity
			17.3.4.2 Alcohol Addiction
			17.3.4.3 Inflammation and Allergy
			17.3.4.4 Infectious Diseases
				Viral Infections
				Bacterial Infections
				Parasite Infections
			17.3.4.5 Embryo Growth
		17.3.5 DNMTi Application in Metabolite Production
		17.3.6 DNMTi in Plants
	17.4 Innovative Indirect and Combined Approaches to Better Target DNA Methylation
		17.4.1 Methyl-CpG Binding Proteins: Nature and Probes
			17.4.1.1 Methyl-CpG Binding Domain Proteins (MBD)
			17.4.1.2 SET and RING Associated (SRA) Domain Proteins
			17.4.1.3 Kaiso Proteins
		17.4.2 Bifunctional Inhibitors Involving DNMTi
	17.5 Limits and Hopes of DNMTi Applications and New Perspectives
	References
18: Gene-Targeted DNA Methylation: Towards Long-Lasting Reprogramming of Gene Expression?
	18.1 Introduction
	18.2 Locus-Specific DNA Methylation Editing
		18.2.1 Targeted DNA Methylation
		18.2.2 Targeted DNA Demethylation
	18.3 Sustained Transcriptional States upon DNA Methylation Editing
		18.3.1 Long-Lasting Transcriptional Repression
		18.3.2 Sustained Gene Re-expression
	18.4 In Vivo Transcriptional Modulation via DNA Methylation Epigenetic Editing
	18.5 Further Considerations
	18.6 Conclusions
	References
19: DNA Labeling Using DNA Methyltransferases
	19.1 Introduction
	19.2 Synthetic Cofactor Analogs for MTase-Directed Modification of DNA
	19.3 MTase Activity with the Synthetic Cofactor Analogs
	19.4 (Towards) Practical Implementation of MTase-Directed DNA Labeling in Genomic Research
		19.4.1 MTase-Directed Labeling for General Manipulations and Analysis of DNA
		19.4.2 DNA Labeling for Analysis of Particular DNA Sites or Sequences
			19.4.2.1 Optical Mapping of DNA Sequences and Epigenetic States
			19.4.2.2 Applications of MTase-Directed Labeling in Epigenomics
	19.5 Cofactor-Independent MTase-Directed Labeling
	19.6 Conclusions/Outlook
	References