UID:
edoccha_9960161395902883
Format:
1 online resource (684 pages)
Edition:
Second edition.
ISBN:
0-12-805477-8
,
0-12-805388-7
Note:
Cover -- Title page -- Copyright page -- Contents -- Contributors -- Preface -- Section I - Overview -- Chapter 1 - An Overview of Epigenetics -- Introduction -- Molecular Mechanisms of Epigenetics -- Methods in Epigenetics -- Model Organisms of Epigenetics -- Factors Influencing Epigenetic Changes -- Evolutionary Epigenetics -- Epigenetic Epidemiology -- Epigenetics and Human Disease -- Epigenetic Therapy -- The Future of Epigenetics -- Conclusions -- References -- Section II - Molecular Mechanisms of Epigenetics -- Chapter 2 - Mechanisms of DNA Methylation and Demethylation During Mammalian Development -- Introduction -- DNA Methylation -- Maintenance DNA Methylation -- DNMT1 -- UHRF1 -- De Novo DNA Methylation -- DNMT3A and DNMT3B -- DNMT3L -- DNA Demethylation -- Passive DNA Demethylation -- Active DNA Demethylation -- TET Proteins -- TET-Dependent Demethylation Pathways -- TET Proteins in Development -- Conclusions -- Glossary -- Abbreviations -- Acknowledgments -- References -- Chapter 3 - Mechanisms of Histone Modifications -- Introduction -- Histone Modifications -- Proline Isomerization -- Citrullination -- Ubiquitination -- Role of Histone Ubiquitination in Transcription Regulation -- Role of Histone Ubiquitination in DNA Damage Response -- Sumoylation -- ADP-Ribosylation -- Phosphorylation -- Role of Histone Phosphorylation in Transcription Regulation -- Role of Histone Phosphorylation in DNA Damage Response -- Methylation -- Role of Histone Methylation in Transcription Regulation -- Role of Histone Methylation in DNA Repair -- Acetylation -- GNAT Superfamily -- MYST Superfamily -- P300/CBP -- Nuclear Hormone-Related HATs -- HAT Complexes -- Histone Deacetylases -- Role of Histone Acetylation in Transcription Regulation -- Role of Histone Acetylation in DNA Repair -- Conclusions -- References.
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Chapter 4 - The Epigenetics of Noncoding RNA -- Introduction -- The Noncoding RNA -- Genetics and Epigenetics -- Epigenetic Regulation of miRNA Expression -- Epitranscriptomics of miRNAs -- Regulation of Epigenetics by miRNAs -- Plausible Interdependence Between miRNA Targeting and mRNA Methylation -- Epigenetic Regulation of lncRNAs -- Epitranscriptomics of lncRNA -- Regulation of Epigenetics by lncRNAs -- Conclusions -- Abbreviations -- Acknowledgments -- References -- Chapter 5 - Prions and Prion-Like Phenomena in Epigenetic Inheritance -- Structural Heredity -- Prions of Saccharomyces cerevisiae and Podospora anserina -- Self Driven Assembly of Hsp60 Mitochondrial Chaperonin -- Cytotaxis of Cilia and Other Complex Structures -- Mixed Heredity: A Prion That Propagates by Covalent Autoactivation -- Regulatory Inheritance -- The Lactose Operon and its Positive Feedback Loop -- Crippled Growth, a Self-Sustained and Mitotically Inheritable Signaling Pathway in the Filamentous Fungus Podospora anserina -- The White/Opaque Switch of Candida albicans, an Epigenetic Switch at the Transcription Level -- Conclusions -- References -- Chapter 6 - Higher-Order Chromatin Organization in Diseases: From Chromosomal Position Effect to Phenotype Variegation -- Introduction -- CPE in Model Organisms -- Telomeric Position Effect -- Setting the Frontiers of Chromatin Domains -- Genome Topology and Scaffolding of Chromosomal Domains -- Boundary Elements are Involved in Functional Genome Partitioning -- Chromosomal Position Effect in Human Pathologies -- Telomeric Position Effect in Human Pathologies -- Conclusions -- References -- Chapter 7 - Polycomb Mechanisms and Epigenetic Control of Gene Activity -- Introduction -- The Hardware -- PRC1 -- PRC2 -- Polycomb Targets -- Drosophila Polycomb Response Elements -- Mammalian PcG Recruitment.
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Other Mechanisms of Recruitment -- Association of PRC2 and PRC1 Complexes -- Mechanisms of PcG Repression -- PRC2 Global Activities -- PRC2 Modulation and Product Feedback Effects -- Higher Order Interactions -- Epigenetic Maintenance or Cellular Memory -- Maintenance of the Nonrepressed State -- The Bivalent State -- Differentiation -- Conclusions -- Abbreviations -- References -- Section III - Methods in Epigenetics -- Chapter 8 - Analysis of Gene-Specific DNA Methylation -- Introduction -- Principles of DNA Methylation Analysis -- Characteristics of Individual Techniques -- Methylation-Sensitive Restriction Enzyme-Based Analyses -- Bisulfite Sequencing -- Combined Bisulfite Restriction Analysis -- Methylation-Specific PCR -- Real-Time MSP -- MethyLight and Digital MethyLight -- Methylation-Sensitive High-Resolution Melting Analysis -- Pyrosequencing -- MassARRAY -- Tips for Individual Methods -- Tips for Bisulfite-Mediated Conversion -- Preparation of Fully Methylated and Fully Unmethylated DNA -- Preparation of Standard DNA -- Tips for Bisulfite Sequencing -- PCR Conditions for Unbiased Amplification -- PCR Cycles to Avoid Artifacts -- Tips for MSP and Quantitative MSP -- Primer Design -- PCR Conditions for Specific Amplification -- Quantity of Template DNA -- Epilogue -- References -- Chapter 9 - Methods for Assessing DNA Cytosine Modifications Genome-Wide -- Introduction -- Techniques Based on Methylation-Sensitive Restriction Endonucleases and PCR -- Targeted and Whole Genome Bisulfite Sequencing -- Infinium Methylation 450 Bead Chip -- Other Sodium Bisulfite-Based Approaches -- Methylated DNA Immunoprecipitation -- MBD Protein-Based Affinity Pulldown -- Methylated-CpG Island Recovery Assay -- 5-Hydroxymethylcytosine Mapping Methodologies -- TET-Assisted Bisulfite Sequencing -- Oxidative Bisulfite Sequencing -- Future Directions and Challenges.
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References -- Chapter 10 - Analyses of Genome-Wide Histone Modifications in the Mammalian Genome -- Introduction -- High-Throughput Technologies to Study Histone Modifications -- ChIP-Seq in Studying Histone Modifications -- Standard ChIP-Seq -- ChIP-Seq With Spike-In Control -- ChIP-Seq With a Limited Number of Cells -- ChIP-Seq With FFPE Samples -- Analyses of Genome-Wide Histone Modification Data -- Genome-wide Profiles and Functions of Histone Modifications -- Histone Methylation -- H3K4me1/2/3 -- H3K9me1/2/3 -- H3K27me1/2/3 -- H3K36me2/3 -- H3K79me1/2/3 -- H4K20me1/2/3 -- Histone Acetylation -- H3K9ac and H4K20ac -- H3K27ac, H3K64ac, H3K122ac, and H4K16ac -- Other Histone Acetylations -- Histone Ubiquitination -- Histone Phosphorylation -- Histone Variants and Linker Histone H1 -- H2A.Z -- MacroH2A -- H3.3 -- Linker Histone H1 -- Chromatin Regulators -- Histone Modifications in Key Genomic Regions -- Histone Modifications in Promoters -- Histone Modifications in Enhancers -- Histone Modifications in Gene Bodies -- Alteration of Histone Modifications in Disease -- Conclusions and Perspectives -- Acknowledgments -- Glossary -- Abbreviations -- References -- Chapter 11 - Techniques for Genome-Wide Expression Analysis of Noncoding RNA -- Introduction -- Mining RNA-SEQ Data for ncRNAs -- Algorithm for Long ncRNA Detection -- Algorithm for Small ncRNA Detection -- Algorithm for circRNA Detection -- cDNA Library Construction -- Ribosomal RNA Depletion of cDNA Libraries -- Library Preparation for Strand-Specific RNA-seq -- Detection of Low-Abundance RNA Species -- Estimating the Transcription and Degradation Rates of Transcripts -- A Genome-Wide Approach to Determine RNA Stability -- Detecting Unstable ncRNAs by Inhibiting the Decay Process of the ncRNAs -- Estimation of the Transcription Rate through Detection of Nascent Transcripts.
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Kinetic Determination of RNA Production and Degradation -- Conclusions -- Glossary -- References -- Chapter 12 - Computational Epigenetics -- Introduction -- Approaches to Measure DNA Methylation and Histone Modifications -- Public Resources for Epigenetic Data -- Bisulfite Sequencing -- Processing Microarray-Based DNA Methylation Data -- Methylated DNA Enrichment -- ChIP-Chip and ChIP Sequencing -- Differentially Methylated Regions -- Prediction of Epigenetic Status -- Integrative Epigenomics -- Concluding Remarks -- Acknowledgments -- References -- Section IV - Model Organisms of Epigenetics -- Chapter 13 - Epigenetic Modifications in Eukaryotes and Prokaryotes are Equally Intriguing -- Introduction -- Biological Significance of Acetylation in Eukaryotic Organisms -- Acetylation of NonHistone Proteins in Regulating Cellular Functions -- Role of Acetylation in Lower Organisms -- Role of Lysine Methylation in Higher Eukaryotes -- Role of Methylation in Lower Organisms -- Role of Deacetylation and Demethylation in Gene Regulation -- Role of Phosphorylation in Higher Eukaryotes -- Role of Phosphorylation in Lower Organisms -- Cross-Talks Between Epigenetic Modifications -- Conclusions and Future Perspectives -- Acknowledgments -- References -- Chapter 14 - Drosophila Epigenetics -- Introduction: Drosophila as a Model Organism in Epigenetic Research -- Epigenetic Modification of Histone Proteins Regulate Chromatin Packaging and Gene Control in Drosophila -- Histone Acetylation -- Histone Methylation -- Position Effect Variegation -- Heterochromatin Within the Drosophila Genome -- Protein Regulators of Position Effect Variegation -- Epigenetic Histone Modifications Regulate PEV in Drosophila -- The Role of Epigenetics During Drosophila Development: Epigenetic Memory.
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Epigenetic Modifications Maintain Patterns of HOX Gene Expression Throughout Drosophila Development.
Language:
English
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