Introduction to Epigenetics.
| Main Author: | |
|---|---|
| Other Authors: | , , |
| Format: | eBook |
| Language: | English |
| Published: |
Cham :
Springer International Publishing AG,
2021.
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| Edition: | 1st ed. |
| Series: | Learning Materials in Biosciences Series
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| Subjects: | |
| Online Access: | Click to View |
Table of Contents:
- Intro
- Preface
- Acknowledgments
- Contents
- 1: Biology of Chromatin
- 1.1 Introduction: Epigenetic Regulation in the Context of the Genome
- 1.1.1 Background: Gene Expression and Chromatin
- 1.1.2 Discovery of the Nucleosomal Structure of the Genome
- 1.2 The Structure of the Nucleosome
- 1.2.1 Histone Variants
- 1.3 Histone Modifications
- 1.3.1 Nomenclature for Histone Modifications
- 1.3.2 Combinatorial Modifications at Pericentric Heterochromatin
- 1.3.3 Histone Modifications at High Resolution
- 1.3.4 Chromatin Modifications Associated with Transcription Units
- 1.3.5 A Concept of Writers, Readers, and Erasers of Histone Modifications
- Method Box 1.1: Chromatin Immunoprecipitation
- 1.4 DNA Modifications
- 1.4.1 DNA Cytosine Methylation
- 1.4.2 DNA Cytosine Hydroxymethylation
- 1.4.3 Interaction of DNA and Histone Modifications
- Method Box 1.2: Analysis of DNA Modifications
- 1.5 Chromatin Organization and Compartmentalization in the Cell Nucleus
- 1.5.1 Replication of Pericentric Heterochromatin Domains
- 1.5.2 Topologically Associating Domains
- 1.5.3 Structural Maintenance of Chromosomes Complexes
- Method Box 1.3: Chromatin Conformation Capture (. Box Fig. 1.3)
- References
- 2: Chromatin Dynamics
- 2.1 Basic Nuclear Activities
- 2.2 Connecting Nucleosomes to DNA Sequence
- 2.3 Nucleosome Remodeling
- 2.3.1 A Template for Transcription
- 2.3.2 Chromatin Remodeling Complexes
- Methods Box 2.1: Determining DNA Accessibility in a Chromatin Template
- 2.4 Nucleosome Assembly
- 2.4.1 Histone Variants and Histone Chaperones
- 2.4.2 The Replication Fork: Still the Major Enigma in Epigenetics
- References
- 3: Cellular Memory
- 3.1 Maintaining Cellular Fates
- 3.2 PcG/TrxG System Maintaining Cellular Memory.
- 3.3 Biochemical Characterization and Molecular Function of PcG/TrxG Proteins
- 3.4 Targeting and Propagation of PcG/TrxG-Controlled Chromatin Domains
- 3.5 Switching Memory and the Role of Non-coding RNAs
- 3.6 Losing Memory
- References
- 4: Dosage Compensation Systems
- 4.1 Introduction: Evolution of Chromosome-Wide Dosage Compensation
- 4.1.1 Consequences of Gene Dosage Differences Arising from Sex Chromosome Erosion
- 4.2 The Dosage Compensation Complex of the Fruit Fly Drosophila melanogaster
- 4.3 X Chromosome Inactivation in Mammals
- 4.3.1 The Mammalian Dosage Compensation Mechanism
- 4.3.2 Regulation of XCI in Different Mammals
- 4.4 X Chromosome Dosage Compensation in Caenorhabditis elegans
- References
- 5: Genomic Imprinting
- 5.1 Discovery of the Non-equivalence of Maternal and Paternal Genomes
- 5.1.1 Genome-Wide Imprinting in Insects
- 5.1.2 Discovery of Genomic Imprinting at an Individual Locus in Maize
- 5.1.3 Demonstrating the Non-equivalence of Parental Genomes in Mammals
- 5.2 Characteristics of Imprinted Genes in Mammals
- 5.2.1 Molecular Characteristics of Imprinted Gene Clusters
- 5.2.2 Molecular Mechanisms Leading to Imprinted Expression
- 5.2.3 The Life Cycle of a Genomic Imprint
- 5.3 Genomic Imprinting and Human Disease
- 5.4 Genomic Imprinting in Flowering Plants
- 5.4.1 Genomic Imprinting Occurs Predominantly in the Endosperm But Also Exists in the Embryo
- 5.4.2 Mechanisms Underlying Imprinting Show Similarities Between Mammals and Plants
- 5.5 Evolution of Genomic Imprinting
- References
- 6: RNA-Based Mechanisms of Gene Silencing
- 6.1 The Unusual Behavior of Transgenes Led to the Discovery of Novel RNA-Based Silencing Mechanisms
- 6.1.1 Conserved Components of RNA-Based Silencing Mechanisms
- 6.2 Post-Transcriptional Gene Silencing (PTGS).
- 6.2.1 The Biogenesis and Function of microRNAs
- 6.2.2 Genome Defense by siRNA-Mediated Silencing
- 6.3 Transcriptional Gene Silencing (TGS)
- 6.4 Paramutation
- 6.4.1 The cis-Regulatory Elements Controlling Paramutation and trans-Acting Factors Link Paramutation to RdDM
- References
- 7: Regeneration and Reprogramming
- 7.1 Types of Regenerative Phenomena
- 7.1.1 Regenerating from a Blastema
- 7.1.2 Changing Potency by Transdifferentiation
- 7.1.3 Signaling in the Blastema
- 7.2 Stem Cells in the Adult
- 7.3 Sources of Pluripotent Stem Cells
- 7.4 Chromatin Dynamics During Reprogramming
- 7.5 Regenerative Therapies
- References
- 8: Epigenetics and Cancer
- 8.1 Epigenetics and Cancer
- 8.2 DNA Methylation and Cancer
- 8.2.1 DNA Hypermethylation in Cancer
- 8.2.2 DNA Hypomethylation in Cancer
- 8.2.3 Loss of Imprinting Through Alterations of DNA Methylation
- 8.2.4 Mutations in the DNA Methylation Machinery in Cancers
- 8.2.4.1 Mutations of de novo DNA Methyltransferase 3a
- 8.2.4.2 Mutations of Ten-Eleven Translocation 2 (TET2)
- 8.2.5 Epigenetic Inhibitors of DNA Methyltransferases in Cancer Therapy
- 8.3 Polycomb Group Proteins and Cancer
- 8.3.1 Alterations of PcG Activity in Cancer
- 8.3.2 Mutations of Affecting Lysine 27 of Histone H3 Occur in Multiple Cancers
- 8.3.3 EZH2 Inhibitors in Cancer Therapy
- 8.4 Histone Acetylation and Deacetylation in Cancers
- 8.4.1 Alterations of Histone Acetyltransferases in Cancer
- 8.4.2 Acetyl-Lysine Recognition Proteins and Cancer
- 8.4.3 Alterations of Histone Deacetylases in Cancer
- 8.4.4 HAT and HDAC Inhibitors in Cancer Therapy
- 8.5 Chromatin Remodeling Factors and Cancer
- 8.5.1 SWI/SNF Complexes and Cancer
- 8.5.2 ISWI Complexes and Cancer
- 8.5.3 The NuRD Complex and Cancer
- 8.5.4 The INO80 Complex and Cancer
- References.
- 9: Epigenetics and Metabolism
- 9.1 Epigenetics and Metabolism
- 9.2 Acetyl-Coenzyme A (Acetyl-CoA)
- 9.2.1 Biosynthesis of Acetyl-CoA
- 9.2.2 Acetyl-CoA as Cofactor of Histone Acetyltransferases
- 9.3 Nicotinamide Adenine Dinucleotide (NAD)
- 9.3.1 Biosynthesis of NAD
- 9.3.2 NAD as Cofactor of Sirtuins and PARPs
- 9.3.2.1 Sirtuins
- 9.3.2.2 PARPs
- 9.4 S-adenosylmethionine (SAM)
- 9.4.1 Biosynthesis of SAM
- 9.4.2 SAM as Cofactor of DNA and Histone Methyltransferases
- 9.5 Flavin Adenine Dinucleotide (FAD)
- 9.5.1 Biosynthesis of FAD
- 9.5.2 FAD as Cofactor of Lysine Demethylase 1 (LSD1)
- 9.6 α-Ketoglutarate (αKG)
- 9.6.1 Biosynthesis of α-Ketoglutarate
- 9.6.2 αKG as Cofactor of TET-Family DNA Demethylases and Jumonji C-Family Histone Demethylases
- References
- Glossary
- Index.