Epigenomics in Health and Disease - 1st Edition - ISBN: 9780128001400, 9780128004968

Epigenomics in Health and Disease

1st Edition

Editors: Mario Fraga Agustin Fernandez
eBook ISBN: 9780128004968
Hardcover ISBN: 9780128001400
Imprint: Academic Press
Published Date: 28th October 2015
Page Count: 328
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Description

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.

Key Features

  • Presents critical reviews that provide the means for reviewing and analyzing the epigenome as a whole, also discussing its translational potential
  • Combines basic epigenomic knowledge with methodological and biostatistical topics related to technology and data analysis
  • Includes coverage of relatively new topics, including DNA methylation dynamics during development and differentiation, genome-wide histone post-translational modifications during development and differentiation, and genome-wide DNA methylation changes during aging

Readership

Graduate students, health care professionals, university researchers, pharmaceutical companies interested in drug development and biotechnology companies. This book could also serve as a core textbook for advanced university or professional school courses with a focus on genetic and/or human diseases.

Table of Contents

  • 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 Factor–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 “OMICS” 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

Details

No. of pages:
328
Language:
English
Copyright:
© Academic Press 2016
Published:
Imprint:
Academic Press
eBook ISBN:
9780128004968
Hardcover ISBN:
9780128001400

About the Editor

Mario Fraga

Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), Universidad de Oviedo, Spain

Affiliations and Expertise

Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), Universidad de Oviedo, Spain

Agustin Fernandez

Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain

Affiliations and Expertise

Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain