Toxicoepigenetics : : Core Principles and Applications.

• Author: McCullough, Shaun D.
• TeilnehmendeR: Dolinoy, Dana.
• Place / Publishing House: San Diego : : Elsevier Science & Technology,, 2018.; Ã2018.
• Year of Publication: 2018
• Edition: 1st ed.
• Language: English
• Physical Description: 1 online resource (430 pages)

Table of Contents

• Front Cover
• Toxicoepigenetics: Core Principles and Applications
• Copyright
• Contents
• Contributors
• Editors' Biography
• Introduction to the Role of the Epigenome in Health and Disease
• Section 1: Histone Modifications and Chromatin Structure
• Chapter 1-1: Role of Histone Acetylation and Acetyltransferases in Gene Regulation
• Introduction
• History and Overview
• Nucleosome Assembly
• Chromatin Folding
• Gene Expression
• DNA Damage Repair
• Toxicoepigenetic Relevance
• Histone Acetyltransferases
• Families and Structures
• Regulation of HATs
• Transcriptional Activation
• HAT Complexes
• SAGA Transcription Regulatory Complex
• NuA4 Transcription Regulatory Complex
• Elongator Complex
• Chromatin Remodeling Complexes
• Global Histone Acetylation
• Role of Histone Acetyltransferases in Gene Activation
• Recruitment of Transcriptional Machinery
• Active Genes
• Inducible/Repressed Genes
• Environmental Exposure
• Histone Deacetylases
• Families
• Catalytic Mechanisms and Structures
• Regulation of HDAC Activity
• Role of HDACs at Active Genes
• Deacetylation and Gene Repression
• HDAC Complexes
• Conclusion and Perspectives
• References
• Chapter 1-2: The Role of Histone Methylation and Methyltransferases in Gene Regulation
• Introduction
• Site Specificity of Histone Methylation
• Lysine Methylation
• H2BK5 Methylation
• H3K4 Methylation
• H3K9 Methylation
• H3K27 Methylation
• H3K36 Methylation
• H3K79 Methylation
• H4K20 Methylation
• H4K5 Methylation
• Arginine Methylation
• Glutamine Methylation
• Regulation of Histone Methylation
• Posttranscriptional Modifications
• Noncoding RNAs
• Regulation of Xenobiotic Biotransformation-Related Genes by Histone Methylation
• Histone Methylation and Human Diseases
• Histone Methylation and Cancer.
• Histone Methylation and Neurological Disorders
• Histone Methylation and Other Diseases
• Histone Methylation and the Toxicity of Chemicals
• Heavy Metals
• Endocrine Disruptors (EDCs)
• Human Genotoxic Chemical Carcinogens From Occupational and Environmental Exposure
• Other Xenobiotics
• Conclusion
• References
• Chapter 1-3: Chromatin Accessibility as a Strategy to Detect Changes Associated With Development, Disease, and Exposure a ...
• Chromatin Accessibility as a Marker of Cell Lineage
• Methods for Determining Chromatin Architecture and Accessibility
• DNase I Hypersensitivity Assays
• Micrococcal Nuclease Assays
• Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE)
• Assay for Transposase-Accessible Chromatin (ATAC)
• Nucleosome Occupancy and Methylome Sequencing (NOMe-seq)
• Single Cell Assays for Determining Chromatin Accessibility in Heterogenous Cell Populations
• Chromatin Accessibility and Disease
• Understanding How Environmental Factors Influence Chromatin Accessibility
• Chromatin Accessibility and Cancer
• Chromatin Signature as a Diagnostic and Therapeutic Target in Cancer
• References
• Further Reading
• Chapter 1-4: Implications for Chromatin Biology in Toxicology
• Changes in Chromatin Modification States Are Important in Aging and the Developmental Origins of Health and Disease
• Mechanisms by Which Toxicant Exposures Alter the Chromatin Landscape
• Repressive Histone Marks and Polycomb Group Proteins
• Xenoestrogens
• Arsenic
• COMPASS Complex
• Xenoestrogens
• Arsenic
• The Histone Methyltransferase G9a
• Phthalates
• Arsenic
• Histone Acetylation
• Organotins
• Phthalates
• Dioxin
• Lead
• Chromium
• Arsenic
• Applications of Chromatin Biology to Toxicological Studies
• Summary
• References
• Section 2: DNA Methylation.
• Chapter 2-1: The Role of DNA Methylation in Gene Regulation
• Chapter Overview
• Introduction
• Mechanisms of DNA Methylation
• De Novo DNA Methylation
• Maintenance DNA Methylation
• DNA Methylation Patterns and the Developing Organism
• X-Chromosome Inactivation
• Imprinted Genes and Development
• Transposable Elements
• DNA Methylation as a Regulator of Gene Expression
• DNA Methylation in Gene Promoters Affects Transcription Factor Binding and Vice Versa
• DNA Methylation Recruits Methyl-CpG Binding Proteins and Remodels Chromatin
• DNA Methylation in the Gene Body Impacts Transcription
• DNA Demethylation
• TET-Mediated Oxidation and Demethylation
• Applications of DNA Methylation in Understanding and Treating Disease
• Environmental Links to DNA Methylation
• DNA Methylation as a Biomarker for Identifying and Understanding Disease
• DNA Methylation in Disease Therapy
• References
• Chapter 2-2: Implications of DNA Methylation in Toxicology
• Introduction
• Detection of DNA Methylation
• Bisulfite Methods of DNA Methylation Detection
• Direct Methods of Locus-Specific or Global DNA Methylation Detection
• Direct Methods of Genome-Wide DNA Methylation Detection
• Principles of DNA Methylation Modification
• Conservation of DNA Methylation Dynamics
• Diet-Induced Changes to DNA Methylation
• Evolutionary Conservation in Diet and DNA Methylation
• Background Diet Considerations in Rodents
• Caloric Restriction and DNA Methylation
• Macronutrient Restriction
• Macronutrient Shifts
• Micronutrient or Trace Mineral Deficiencies
• Pharmaceuticals
• Metals
• Metals as Toxicants
• High Density Metals
• Light Metals
• Organic Toxicants
• Nonchemical Stress
• Future Directions
• References
• Chapter 2-3: DNA Methylation as a Biomarker in Environmental Epidemiology.
• Methylomics as a Potential Biomarker for Both Disease and Toxic Exposures
• Methylomics of WBCs in Relation to Disease Causation and Toxic Exposures
• Methodological Considerations in Methylome-Wide Association Studies
• Platforms That Assess Single-Base Resolution Methylation
• Array-Based: MethylationEPIC BeadChip (Infinium) Microarray
• Next-Generation Sequencing
• Preprocessing and Normalization
• MethylationEPIC BeadChip (Infinium) Microarray
• Bisulfite Sequencing
• Addressing Confounding
• Inclusion of Technical Replicates
• Calculation for Differentially Methylated Sites
• Calculation for Differentially Methylated Regions
• Methylomics as a Potential Biomarker for Both Disease and Toxic Exposures
• Example: Smoking and AHRR Methylation
• Example: Air Pollution and DNA Methylation
• Example: Biological Aging as Measured by the Epigenetic Clock
• Example: VTRNA2-1 as a Metastable Epiallele
• Example: Epigenetic Pathway Linking Prenatal Maternal Stress and Wheeze in Children
• Conclusion
• References
• Chapter 2-4: DNA Hydroxymethylation: Implications for Toxicology and Epigenetic Epidemiology
• Introduction
• Chemistry of DNA Hydroxymethylation
• The Sixth-Base of Cytosine
• Distribution of 5-hmC in the Genome
• Changes in 5-hmC Level During Development
• Measurement of 5-hmC
• Global 5-hmC Measurement
• Locus-Specific 5-hmC Measurement
• DNA Immunoprecipitation (DIP)
• Enzymatic and Chemical Modifications
• Single Molecule Detection
• Exposures to Environmental Toxicants/Stressors and Changes in 5-hmC
• Heavy Metals
• Environmental Estrogens
• Air Pollutants
• Pesticides
• Ionizing Radiation
• Lifestyle
• Aging
• Discussion and Future Directions
• Acknowledgments
• References
• Section 3: Noncoding RNAs
• Chapter 3-1: The Role of Noncoding RNAs in Gene Regulation
• Introduction.
• Overview of Noncoding RNAs
• Transfer and Ribosomal RNA
• Long Noncoding RNA (lncRNA)
• Competitive Endogenous RNA
• Long Intervening Noncoding RNA
• Enhancer RNA
• Short Noncoding RNA
• Piwi-Interacting RNA
• Small Nuclear RNA
• Short Nucleolar RNA
• MicroRNA
• Short Interfering RNA
• MicroRNA Discovery
• MicroRNA Biogenesis and Regulation
• Pri-miRNA Transcription and Regulation
• Pri-miRNA Processing and Nuclear Export
• Maturation of miRNA RISC Formation
• Regulation of Mature miRNA by ceRNA
• Biological Roles of MicroRNA
• Gene Target Silencing
• Target Degradation Pathway
• Translational Repression
• miRNA-Mediated Gene Target Upregulation
• Enhanced Biological Impact of miRNAs Through Feedback Loops
• Positive Feedback Loop
• Negative Feedback Loop
• Switching Loops
• Biofluid-Based Biomarkers and Cell Communication
• Concluding Remarks and Future Directions
• Acknowledgments
• References
• Chapter 3-2: miRNAs and lncRNAs as Biomarkers of Toxicant Exposure
• Introduction
• miRNAs and Toxicological Response to Chemicals
• Endocrine Disruptor Chemicals and Altered miRNA Profile
• Bisphenol A
• Phthalates
• Exposure to Metals
• Exposure to Particles
• Nanoparticles
• Cigarette Smoking
• lncRNAs and Toxicological Response to Chemicals
• Endocrine Disruptor Chemicals and Altered lncRNA Profile
• Bisphenol A
• Exposure to Metals and lncRNA Expression
• Cigarette Smoking and lncRNA Profile
• Summary
• References
• Further Reading
• Section 4: Special Considerations in Toxicoepigenetics Research
• Chapter 4-1: Germline and Transgenerational Impacts of Toxicant Exposures
• Introduction
• The Germline
• Germline Specification and the Importance of the Epigenetic Repression of Somatic Fates
• PGC's Epigenetic Reprogramming: A Critical Period.
• Transgenerational Effects Stemming From Environmental Exposures.