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Handbook of epigenetics : the new molecular and medical genetics / edited by Trygve O. Tollefsbol.
- Format:
- Book
- Language:
- English
- Subjects (All):
- Epigenetics--Periodicals.
- Epigenetics.
- Epigenetics--Handbooks, manuals, etc.
- Epigenesis, Genetic.
- Epigenomics--methods.
- Medical Subjects:
- Epigenesis, Genetic.
- Epigenomics--methods.
- Physical Description:
- 1 online resource (684 pages)
- Edition:
- Second edition.
- Place of Publication:
- London, England : Academic Press, 2017.
- Summary:
- Handbook of Epigenetics: The New Molecular and Medical Genetics, Second Edition, provides a comprehensive analysis of epigenetics, from basic biology, to clinical application.
- Contents:
- 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
- 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
- Glossary
- Abbreviations
- Acknowledgments
- Chapter 3 - Mechanisms of Histone Modifications
- 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
- References.
- Chapter 4 - The Epigenetics of Noncoding RNA
- 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
- 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
- Chapter 6 - Higher-Order Chromatin Organization in Diseases: From Chromosomal Position Effect to Phenotype Variegation
- 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
- Chapter 7 - Polycomb Mechanisms and Epigenetic Control of Gene Activity
- The Hardware
- PRC1
- PRC2
- Polycomb Targets
- Drosophila Polycomb Response Elements
- Mammalian PcG Recruitment.
- 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
- Section III - Methods in Epigenetics
- Chapter 8 - Analysis of Gene-Specific DNA Methylation
- 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
- Chapter 9 - Methods for Assessing DNA Cytosine Modifications Genome-Wide
- 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.
- References
- Chapter 10 - Analyses of Genome-Wide Histone Modifications in the Mammalian Genome
- 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
- Chapter 11 - Techniques for Genome-Wide Expression Analysis of Noncoding RNA
- 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.
- Kinetic Determination of RNA Production and Degradation
- Chapter 12 - Computational Epigenetics
- Approaches to Measure DNA Methylation and Histone Modifications
- Public Resources for Epigenetic Data
- 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
- Section IV - Model Organisms of Epigenetics
- Chapter 13 - Epigenetic Modifications in Eukaryotes and Prokaryotes are Equally Intriguing
- 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
- 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
- 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.
- Epigenetic Modifications Maintain Patterns of HOX Gene Expression Throughout Drosophila Development.
- Notes:
- Includes bibliographical references at the end of each chapters and index.
- Description based on online resource; title from PDF title page (ebrary, viewed August 9, 2017).
- Description based on publisher supplied metadata and other sources.
- ISBN:
- 0-12-805477-8
- 0-12-805388-7
- OCLC:
- 993772349
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