Introduction to Epigenetics.

Introduction to Epigenetics.

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Bibliographic Details
Superior document:Learning Materials in Biosciences Series
:
Paro, Renato.
TeilnehmendeR:
Grossniklaus, Ueli.
Santoro, Raffaella.
Wutz, Anton.
Place / Publishing House:Cham : : Springer International Publishing AG,, 2021.
©2021.
Year of Publication:2021
Edition:1st ed.
Language:English
Series:Learning Materials in Biosciences Series
Online Access:
Physical Description:1 online resource (219 pages)
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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.

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