Cover -- Title Page -- Copyright -- Dedication -- Preface -- Acknowledgments -- List of Contributors -- Chapter 1: Introduction -- References -- Chapter 2: Environment, Epigenetics, and Diseases -- 2.1 Perceptions of epigenetics -- 2.2 Environmental epigenetics and human diseases -- 2.3 Implications of environmental epigenetics and future prospects -- 2.4 Key questions to be answered -- Acknowledgments -- References -- Chapter 3: DNA Methylation and Toxicogenomics -- 3.1 Introduction -- 3.2 Toxicology -- 3.3 Toxicogenomics -- 3.4 Epigenetics -- 3.5 DNA methylation -- 3.6 DNA methyltransferases -- 3.7 DNA methylation is alteres upon exposure to chemicals and toxins -- 3.8 Toxicogenomics and epigenetics -- 3.9 Hydroxymethyl cytosine and toxicogenomics -- 3.10 MicroRNAs -- 3.11 DNA methylation in cancer -- 3.12 Bioinformatics approach -- 3.13 Summary -- Acknowledgments -- References -- Chapter 4: Chromatin at the Intersection of Disease and Therapy -- 4.1 Epigenetic marks on chromatin: a complex pathway with high flexibility -- 4.2 Epigenetic approaches to treatment of cancer -- 4.3 Epigenetic modifications and potential therapy in other diseases -- 4.4 Conclusion -- References -- Chapter 5: Molecular Epigenetic Changes Caused by Environmental Pollutants -- 5.1 Introduction -- 5.2 Mechanisms of molecular epigenetic changes -- 5.3 Epigenetic assays -- 5.4 Epigenetic changes induced by organic chemicals -- 5.5 Epigenetic changes induced by metals -- 5.6 Concluding remarks -- References -- Chapter 6: Epigenetic Mediation of Environmental Exposures to Polycyclic Aromatic Hydrocarbons -- 6.1 Introduction -- 6.2 Epigenetic modifications: DNA methylation -- 6.3 DNA methylation and cancer -- 6.4 Epigenetic histone modifications -- 6.5 Benzo(a)pyrene - a prototype PAH and environmental carcinogen.

6.6 Molecular mechanisms of benzopyrene carcinogenicity: geno- and epigeno-toxicity -- 6.7 Epigenetic effects of multiple/synergistic carcinogen exposures -- 6.8 Summary and future considerations -- Acknowledgments -- References -- Chapter 7: Epigenomic Actions of Environmental Arsenicals -- 7.1 Introduction -- 7.2 Arsenicals in relation to human health -- 7.3 Arsenical mechanisms of action -- 7.4 Models to study arsenical action -- 7.5 Models used to study epigenetic action -- 7.6 Epigenetic effects of arsenicals -- 7.7 Perspectives -- References -- Chapter 8: Arsenic-Induced Changes to the Epigenome -- 8.1 Introduction -- 8.2 Arsenic exposure and DNA methylation -- 8.3 DNA methylation changes associated with arsenic exposure -- 8.4 Histone modifications associated with arsenic exposure -- 8.5 MicroRNA (miRNA) alterations associated with arsenic exposure -- 8.6 Conclusions and future directions -- Acknowledgments -- References -- Chapter 9: Environmental Epigenetics, Asthma, and Allergy: Our Environment's Molecular Footprints -- 9.1 Introduction -- 9.2 Asthma environmental toxicants associated with epigenetic regulation -- 9.3 Epigenetic changes and asthma phenotype -- 9.4 'Pharmacoepigenetics' -- 9.5 Conclusion -- References -- Chapter 10: miRNAs in Human Prostate Cancer -- 10.1 Introduction -- 10.2 Biogenesis, function, and target of miRNA -- 10.3 miRNA and human cancer -- 10.4 miRNAs as oncogenes and tumor suppressors -- 10.5 Expression profile of miRNA in prostate cancer -- 10.6 miRNA as therapeutic targets for prostate cancer -- 10.7 Conclusion and future directions -- References -- Chapter 11: Environment, Epigenetics, and Cardiovascular Health -- 11.1 Introduction -- 11.2 Epidemiological evidence of environmental factors affecting cardiovascular health.

11.3 Cause and effect relation between environmental exposure and cardiovascular diseases -- 11.4 Cardiovascular epigenetic signatures as risk factors and biomarkers for environmental exposure -- 11.5 Conclusion -- References -- Chapter 12: Toxicology, Epigenetics, and Autoimmunity -- 12.1 Introduction -- 12.2 Drugs and toxicants in epigenetics -- 12.3 Metabolic requirements for epigenetics -- 12.4 Autoimmunity and epigenetics -- 12.5 Conclusion -- References -- Chapter 13: Toxicoepigenomics in Lupus -- 13.1 Introduction -- 13.2 Etiology of lupus -- 13.3 Epigenetics and lupus -- 13.4 Environmental contributions to lupus -- 13.5 Summary -- References -- Chapter 14: Ocular Epigenomics: Potential Sites of Environmental Impact in Development and Disease -- 14.1 Introduction -- 14.2 Gene expression in ocular development -- 14.3 Epigenetic regulation in ocular development -- 14.4 DNA-methylation changes in ocular disease -- 14.5 Inherited and age-related diseases of the eye -- 14.6 Pharmacological effects on retinal function -- 14.7 Future research -- References -- Chapter 15: Nuclear RNA Silencing and Related Phenomena in Animals -- 15.1 Introduction -- 15.2 Conclusion -- Acknowledgments -- References -- Chapter 16: Epigenetic Biomarkers in Cancer Detection and Diagnosis -- 16.1 DNA methylation -- 16.2 Epigenetics of cancer -- 16.3 Epigenetic biomarkers for cancer diagnostics: DNA methylation -- 16.4 Application of aberrant DNA methylation to cancer diagnostics -- 16.5 Epigenetic biomarkers in breast cancer -- 16.6 Epigenetic biomarkers in prostate cancer -- 16.7 Epigenetic biomarkers in lung cancer -- 16.8 Epigenetic biomarkers in colorectal cancer -- 16.9 Epigenetic biomarkers in liver cancer -- 16.10 Cancer detection and diagnosis -- References -- Chapter 17: Epigenetic Histone Changes in the Toxicologic Mode of Action of Arsenic -- 17.1 Introduction.

17.2 Epigenetics and cancer -- 17.3 Epigenetics effects of arsenic -- 17.4 Conclusions -- References -- Chapter 18: Irreversible Effects of Diethylstilbestrol on Reproductive Organs and a Current Approach for Epigenetic Effects of Endocrine Disrupting Chemicals -- 18.1 Introduction -- 18.2 Adverse effects of perinatally-exposed DES on the mouse vagina -- 18.3 MeDIP-ChIP -- 18.4 Future research needs -- Acknowledgments -- References -- Chapter 19: Epigenomics - Impact for Drug Safety Sciences -- 19.1 Introduction - the dynamic epigenome and perturbations in disease -- 19.2 Relevance of epigenetics for toxicology -- 19.3 Towards identifying epigenetic biomarkers of drug-induced toxicity -- 19.4 Challenges of integrating epigenetic analysis into toxicity testing -- 19.5 Practical considerations -- 19.6 Bioinformatics and modeling of epigenomic data -- 19.7 Case study: identification of early mechanism and biomarkers for non-genotoxic carcinogenesis (NGC) -- 19.8 Conclusions -- Acknowledgments -- References -- Chapter 20: Archival Toxicoepigenetics: Molecular Analysis of Modified DNA from Preserved Tissues in Toxicology Studies -- 20.1 Introduction -- 20.2 Preservation of tissue: effects on protein and nucleic acids -- 20.3 Extraction of nucleic acids from fixed or embedded tissues -- 20.4 Analysis of methylated DNA for epigenetics -- 20.5 Survey of epigenetic studies using formalin preserved tissues -- 20.6 Prospects for toxicoepigenetics in preserved tissues -- 20.7 Conclusion -- References -- Chapter 21: Nanoparticles and Toxicoepigenomics -- 21.1 Nanoparticles -- 21.2 Particles and the environment -- 21.3 Nanoparticles in soil -- 21.4 Nanoparticles in water -- 21.5 Nanoparticles in air -- 21.6 Nanoparticles in medicine -- 21.7 Nanotoxicology -- 21.8 Nanotoxicology in humans and experimental animals -- 21.9 Complications with nanotoxicological studies.

21.10 Molecular mechanisms of nanoparticle toxicity and cellular defense mechanisms -- 21.11 Molecular mechanisms of nanoparticle-induced cytotoxicity -- 21.12 Nano-epigenomcs and epigenetics -- 21.13 Conclusion -- References -- Chapter 22: Methods of Global Epigenomic Profiling -- 22.1 Introduction -- 22.2 DNA methylation -- 22.3 Histone modifications and chromatin remodeling -- 22.4 Noncoding RNA -- 22.5 Summary and discussion -- Acknowledgments -- References -- Chapter 23: Transcriptomics: Applications in Epigenetic Toxicology -- 23.1 Introduction -- 23.2 Microarray analysis of gene expression profiles -- 23.3 Gene expression studies - challenges -- 23.4 Conclusions -- Acknowledgments -- Disclaimer -- References -- Chapter 24: Carcinogenic Metals Alter Histone Tail Modifications -- 24.1 Introduction -- 24.2 Epigenetics and histone tail modifications -- 24.3 Arsenic -- 24.4 Nickel -- 24.5 Hexavalent chromium (Cr [VI]) -- 24.6 Cadmium -- 24.7 Summary -- References -- Chapter 25: Prediction of Epigenetic and Stochastic Gene Expression Profiles of Late Effects after Radiation Exposure -- 25.1 Introduction - pathological profiling (diagnostic endpoint) and toxicological profiling (probabilistic endpoint) -- 25.2 Radiation exposure and dosimetric quantum biology -- 25.3 Common gene expression profiles after subacute and prolonged effects after radiation exposure -- 25.4 Stochastic expression gene profiles after radiation exposure -- 25.5 Conclusions -- Appendix A -- Appendix B -- Appendix C -- References -- Chapter 26: Modulation of Developmentally Regulated Gene Expression Programs through Targeting of Polycomb and Trithorax Group Proteins -- 26.1 Introduction -- 26.2 Polycomb group (PcG) proteins -- 26.3 Trithorax group genes -- 26.4 Model for the transcriptional regulation of developmentally regulated genes by PcG and TrxG.

26.5 PcG and TrxG proteins in disease.