Epigenomics in Health and Disease

1st Edition - October 12, 2015
Editors: Mario Fraga, Agustin Fernandez Fernandez
Language: English
Hardback ISBN:
9 7 8 - 0 - 1 2 - 8 0 0 1 4 0 - 0
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 0 0 4 9 6 - 8

Epigenomics in Health and Disease discusses the next generation sequencing technologies shaping our current knowledge with regards to the role of epigenetics in normal developme… Read more

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Epigenomics in Health and Disease
discusses the next generation sequencing technologies shaping our current knowledge with regards to the role of epigenetics in normal development, aging, and disease.

It includes the consequences for diagnostics, prognostics, and disease-based therapies made possible by the study of the complete set of epigenetic modifications to the genetic material of human cells.

With coverage pertinent to both basic biology and translational research, the book will be of particular interest for medical and bioscience researchers and students seeking current translational knowledge in epigenesis and epigenomics.

Coverage includes the latest findings on epigenome-wide research in disease-based profiling, epidemiological implications, epigenome-wide epigenetic studies, the cancer epigenome, and other pervasive disease categories.

List of Contributors
Preface
Chapter 1. The Role of the Genetic Code in the DNA Methylation Landscape Formation
- Abstract
- 1.1 Bringing the Genetic Code to Life
- 1.2 Intrinsic Properties of DNA
- 1.3 Sequence-Pattern-Dependent DNA Methylation Profiles
- 1.4 DNA-Binding Factors Shaping the Epigenetic Landscape
- 1.5 The Dynamics of Transcription-Factor-Mediated DNA hypomethylation
- 1.6 Translational Potential of Demethylation Dynamics
- 1.7 DNA Methylation Quantitative Trait Loci
- 1.8 Genotype-Driven Variance in Human DNA Methylation Profiles
- 1.9 Epigenetic Mediator Function for Human Risk Phenotype Formation
- 1.10 Epitype Association Guiding the Interpretation of Cancer Risk Polymorphisms
- 1.11 Closing Remarks
- References
Chapter 2. DNA Methylation Microarrays
- Abstract
- 2.1 Introduction
- 2.2 Infinium DNA Methylation Technology
- 2.3 HumanMethylation450 Array Design and Performance
- 2.4 HumanMethylation450 Array Advantages and Limitations
- 2.5 DNA Methylation Data Analysis
- 2.6 Use of Methylation Arrays in Epigenetic Studies
- 2.7 Conclusion
- References
Chapter 3. Ultra-Deep Sequencing of Bisulfite-Modified DNA
- Abstract
- 3.1 Introduction
- 3.2 Sample Preparation and Study Design Considerations for Ultra-Deep Bisulfite Sequencing
- 3.3 Technical Considerations for Ultra-Deep Bisulfite Sequencing Approaches
- 3.4 Testing for Differential Methylation
- 3.5 Identifying Enriched or Differentially Methylated Transcription Factorâ€“Binding Sites
- 3.6 Data Visualization and Annotation
- 3.7 Gene Set Enrichment Strategies
- 3.8 Published Applications
- 3.9 Conclusions and Future Directions
- References
Chapter 4. Bioinformatics Tools in Epigenomics Studies
- Abstract
- 4.1 Introduction
- 4.2 Types of Experiments and Data Characteristics
- 4.3 Bioinformatics Tools
- 4.4 Reproducible Research
- 4.5 Conclusion
- References
Chapter 5. Noncoding RNA Regulation of Health and Disease
- Abstract
- 5.1 Introduction
- 5.2 Noncoding RNAs
- 5.3 Circulating Noncoding RNAs
- 5.4 Exosomes: Biogenesis and Cancer Biomarkers
- 5.5 Conclusion
- References
Chapter 6. Genome-Wide DNA Methylation Changes During Aging
- Abstract
- 6.1 Introduction
- 6.2 Observed Differences in DNA Methylation Patterns with Aging
- 6.3 Causes of Age-Related DNA Methylation Changes
- 6.4 Tissue-Specific and Tissue-Independent Age-Associated DNA Methylation
- 6.5 Implications: Age-Associated DNA Methylation and Disease Risk
- 6.6 Environmental Factors that Influence DNA Methylation Patterns Over Time
- 6.7 DNA Methylation as an Epigenetic/Biologic Clock
- 6.8 Summary and Future Studies
- References
Chapter 7. The Dynamics of Histone Modifications During Aging
- Abstract
- 7.1 Introduction
- 7.2 Part 1: Nucleosome Density and Aging
- 7.3 Part 2: Histone Variants
- 7.4 Part 3: Histone Modifications
- 7.5 Progeria: Accelerated Aging Due to Nuclear Architecture Dysfunction
- 7.6 Conclusion
- References
Chapter 8. Epigenomic Studies in Epidemiology
- Abstract
- 8.1 Introduction: From Classical Epidemiology to Epigenomic Epidemiology
- 8.2 The Choice of an Appropriate Study Design
- 8.3 Environmental Epigenetics
- 8.4 Validation of Results
- 8.5 Biologic Sample Selection
- 8.6 Methods Selection
- 8.7 Extracellular Nucleic Acid Markers
- 8.8 Sample Size Selection and Statistics
- 8.9 Confounding Factors and Effect Modifiers: Dealing with Complex Systems
- 8.10 Conclusions and Perspectives
- References
Chapter 9. The DNA Methylomes of Cancer
- Abstract
- 9.1 Introduction to the Epigenetic Language
- 9.2 Definition and Classical Roles of DNA Methylation
- 9.3 DNA Methylation in Cancer: A Historical Perspective
- 9.4 High-Throughput Approaches to Detect DNA Methylation Changes
- 9.5 The Genome-Wide DNA Methylome of Cancer Cells: Overview and General Insights
- 9.6 DNA Methylation Changes Outside Promoters Is a Major Finding in Cancer
- 9.7 Altered DNA Methylation in Cancer Is Biased Toward Particular Chromatin States
- 9.8 Normal Reference Samples of the Cancer Epigenome
- 9.9 DNA Methylation Changes: Cause or Consequence of Cancer?
- 9.10 Clinical Use of DNA Methylation in Cancer
- 9.11 Conclusions and Future Directions
- Acknowledgments
- References
Chapter 10. Genome-Wide Epigenetic Studies in Neurologic Diseases
- Abstract
- 10.1 Introduction
- 10.2 Neuroepigenetics in the â€œOMICSâ€ Era
- 10.3 Conclusion
- References
Chapter 11. Epigenetic Deregulation in Autoimmune Disease
- Abstract
- 11.1 The Loss of Immune Tolerance: Breaking Bad
- 11.2 Epigenetic Regulation
- 11.3 Local and Systemic Autoimmune Disorders: Importance of the Environment
- 11.4 Epigenetic Regulation in Autoimmune Disorders
- 11.5 Molecular Characterization of Common Pathogenic Routes: Autoimmunity in the Twenty-First Century
- 11.6 Conclusions and Perspectives
- References
Chapter 12. Genome-Wide DNA and Histone Modification Studies in Metabolic Disease
- Abstract
- 12.1 Introduction
- 12.2 Type 2 Diabetes and Epigenetic Modifications
- 12.3 Obesity and Epigenetic Modifications
- 12.4 Do Diet and Exercise Interventions Alter the Epigenetic Pattern and Potentially Risk for Metabolic Disease?
- 12.5 Does the Intrauterine Environment Alter the Epigenetic Pattern and Potentially Risk for Metabolic Disease?
- 12.6 Conclusions
- References
Chapter 13. Clinical Applications of Epigenomics
- Abstract
- 13.1 Introduction
- 13.2 Cancer Is an Epigenetic Disease
- 13.3 Epigenomics as a Tool to Unravel Cancer Mechanisms
- 13.4 Methylation Profiling in Other Cancers
- 13.5 Methylation Markers as Clinical Predictors of Disease Progression and the Potential Power of Quantitative Biomarkers
- 13.6 Genetic Mutation in Epigenetic Regulators
- 13.7 Other Epigenetic Methylation Patterns in Cancer
- 13.8 Other Recurrent Epigenomic Patterns in Cancer (Nonmethylation)
- 13.9 Epigenomics and Epigenetic Therapy
- 13.10 Potential Applications of Epigenetic and Genetic Biomarkers with Epigenetic Therapies
- 13.11 Epigenome-Wide Association Studies for Common Human Diseases
- 13.12 Summary and Future Directions Related to Clinical Applications of Epigenomics
- References
Index

Life Sciences

Physical Sciences & Engineering

Social Sciences & Humanities

Health

Epigenomics in Health and Disease

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Mario Fraga

Agustin Fernandez Fernandez