Note: Intro -- Epigenetics in Organ Specific Disorders -- Copyright -- Contents -- Contributors -- Chapter 1 Introduction-Epigenetic regulations in organ specific disorders -- 1 Overview of epigenetics in organ-specific disorders -- 2 Epigenetics in human diseases/disorders -- 2.1 Epigenetic influences on cellular functions -- 2.1.1 Tissue fibrosis -- 2.1.2 Vascular stenosis -- 2.1.3 Tumor metastasis -- 2.2 Epigenetic mechanisms in cellular dedifferentiation -- 2.3 Epigenetic mechanisms in autophagy-mediated cell survival -- 3 Current progress on "epigenetic drugs" -- 4 About the chapters described in this book -- References -- Section 1 Molecular and structural epigenetics -- Chapter 2 Higher-order chromatin structure and gene regulation -- 1 Introduction -- 2 Chromatin structure -- 2.1 Nucleosomes and the factors that regulate their dynamics -- 2.2 How the nucleosomes are (not) organized -- 2.3 Chromatin loops -- 2.4 Chromatin remodelers -- 2.5 Chromosome compartmentalization -- 3 Roles of enhancers in cell type-specific gene expression -- 3.1 General features -- 3.2 Classification of enhancer states -- 3.3 Enhancer grammar -- 3.4 Evolution of enhancers -- 3.5 Enhancer-promoter interactions -- 3.6 Super-enhancers -- 3.7 Insulated neighborhoods -- 3.8 Cell type-specific variation of chromatin structure -- 4 Concluding remarks -- References -- Chapter 3 Molecular and structural interactions between epigenetic regulators -- 1 Introduction -- 2 DNMTs as epigenetic regulators -- 2.1 Protein-interacting domains of DNMT1 -- 2.2 Interactions between DNMT1 and UHRF1 -- 2.3 Indirect regulatory functions of UHRF1 on DNA methylation -- 2.4 Molecular interactions between DNMT1 and other cellular proteins -- 2.5 Functions of structural domains in de novo methyltransferases -- 2.6 Functional significance and molecular interactions of DNMT3A and DNMT3B. , 2.7 Mutations affecting molecular interactions of DNMT3A and DNMT3B -- 3 Unique role of UHRF1 in directing DNMT1 -- 4 HDACs as epigenetic gene regulators -- 5 Conclusions -- References -- Section 2 Epigenetic effects on cell fate -- Chapter 4 Epigenetic regulation of necrosis and pyknosis -- 1 Introduction -- 2 DNA methylation and necrosis -- 3 Histone modification and higher order chromatin remodeling in necrosis -- 4 The role of noncoding RNA in necrosis -- 5 Pyknosis: Nuclear morphological changes in cell death -- 5.1 Apoptotic pyknosis -- 5.2 Necrotic pyknosis -- 5.3 Epigenetic regulation of pyknosis -- 6 Conclusion -- References -- Chapter 5 HDAC inhibition in cancer -- 1 Epigenetics and major epigenetic alterations -- 1.1 Introduction to epigenetics -- 1.1.1 Histones in epigenetics -- 1.1.2 Types of chromatin modifications -- 1.1.3 DNA methylation -- 1.1.4 Methylations and acetylations of histones -- 1.1.5 Phosphorylation of histones -- 1.1.6 Histone acetyl transferase (HAT) -- 1.1.7 HAT inhibitors -- 1.2 Histone deacetylases -- 1.2.1 Histone deacetylation by histone deacetylases (HDACs) -- 2 HDACs, HDACIs, and cell cycle regulation -- 2.1 HDACs and cell cycle -- 2.1.1 Modulation of cell cycle by HDACs -- 2.1.2 HDACs and p53 -- 2.1.3 HDACs and p21 -- 2.2 Inhibition of histone deacetylases -- 2.2.1 HDAC inhibition and cellular mechanisms -- 2.3 Histone deacetylase inhibitors (HDACIs) -- 2.3.1 Suberoylanilide hydroxamic acid -- 2.3.2 Trichostatin A -- 2.3.3 Valproic acid -- 2.3.4 Suberic bis-hydroxamic acid -- 2.3.5 Panobinostat -- 2.3.6 Sodium butyrate -- 2.3.7 Cell cycle arrest by HDACIs -- 2.3.8 HDACI induction of p21WAF1/CIP1 -- 2.3.9 HDACI treatment disrupts mitosis and the mitotic checkpoint -- 2.4 HDACIs and cell death -- 2.4.1 Sensitivity for HDACIs and correlation to apoptosis -- 2.4.2 HDACI-induced necroptosis. , 2.4.3 Cell differentiation induced by HDACIs -- 2.4.4 Inhibition of DNA repair -- 3 Epigenetics and cancer -- 3.1 Epigenetic modifications in cancer and cancer growth -- 3.2 Epigenetic changes in prostate cancer -- 3.3 Histone acetylation and deacetylation in breast cancer -- References -- Chapter 6 Epigenetic signatures that maintain stemness in pluripotent and mesenchymal stem cells -- 1 Introduction -- 2 Chromatin reorganization -- 2.1 Polycomb and Trithorax complexes -- 2.2 ATP-based chromatin remodeling -- 2.2.1 SWI/SNF -- 2.2.2 ISWI -- 2.2.3 CHD -- 2.2.4 INO80 -- 3 DNA methylation -- 4 TET proteins -- 5 Histone variants -- 6 Histone modifications -- 6.1 Histone methylation -- 6.2 Histone acetylation -- 6.3 Histone phosphorylation -- 7 Conclusion -- References -- Chapter 7 Epigenetic modifications and alternative pre-mRNA splicing in cancer -- 1 Introduction -- 2 Alternative splicing: An overview -- 2.1 The history of alternative splicing -- 2.2 The types and mechanisms of alternatively spliced events -- 3 A simplistic overview on epigenetics -- 3.1 DNA methylation -- 3.2 Posttranslational histone modifications -- 3.3 Nucleosome remodeling -- 3.4 Noncoding RNAs -- 4 The epigenetics whereabouts in cancer -- 5 The epigenetically controlled alternative splicing in cancer -- 5.1 Cotranscriptional coupling of alternative splicing events -- 5.2 Reorganized chromatin promotes cancer-specific splicing -- 5.3 Reformed nucleosome positioning -- 5.4 DNA methylation in tumorigenesis -- 5.5 Tailored histone modifications promote cancer -- 6 Implications of epigenetics in anticancer therapy -- 7 Conclusions -- References -- Section 3 Epigenetic regulations in infections and immune responses -- Chapter 8 Epigenetics of T cell - mediated immunological responses -- 1 Introduction -- 2 Epigenetics of T cell immunity. , 2.1 Epigenetic factors and T cell development -- 2.2 Epigenetics of T cell plasticity -- 2.3 miRNAs in T cell development -- 3 Epigenetics in allergy and inflammatory diseases -- 3.1 Epigenetics in asthma -- 3.1.1 Childhood asthma -- 3.1.2 Adult asthma -- 3.1.3 Histone modifications in asthma -- 3.1.4 Role of miRNAs in asthma -- 3.2 Epigenetics in atopic dermatitis -- 3.3 Other allergies -- 4 Epigenetics in autoimmunity -- 4.1 DNA methylation -- 4.2 DNA hydroxymethylation -- 4.3 Histone modifications -- 4.4 Methylation of retroelements -- 5 Conclusion -- References -- Chapter 9 Epigenetic modifications and regulation in infection -- 1 Introduction -- 2 Viral infections -- 2.1 DNA hypomethylation -- 2.2 Histone mimicry -- 2.3 Epigenetic modifications of host antiviral responses -- 2.4 Epigenetics and latency -- 2.5 Epigenetic regulation of ACE2 in SARS-CoV-2 infection -- 2.6 Epigenetics and viral oncogenesis -- 3 Bacterial infections -- 3.1 Methylation of bacterial genes -- 3.2 Methylation and acetylation of host genes in bacterial infection -- 4 Trained immunity and epigenetics -- 4.1 Trained innate immunity -- 4.2 Epigenetic changes associated with trained immunity -- 4.3 Role of vaccinations in trained immunity -- 4.4 Epigentic regulation via metabolic pathways in infections -- References -- Section 4 Epigenetic influences on aging, diseases, and diet -- Chapter 10 Epigenetics of aging -- 1 Introduction -- 2 Epigenetics, disease, and aging -- 2.1 DNA modifications -- 2.2 Histone modifications -- 2.3 Chromatin remodeling -- 2.4 Noncoding RNAs -- 2.5 RNA methylation -- 3 Cancer -- 4 Neurodegeneration -- 5 Cardiovascular disease -- 6 Conclusions and future perspectives -- References -- Chapter 11 Epigenetic regulation mediated by diets -- 1 Introduction -- 1.1 Effects of diet on epigenetics and health. , 1.1.1 Effects of specific nutrients on specific epigenetic mechanisms -- 1.2 Impact of diet on fetal epigenetics -- 1.2.1 Early-life nutritional exposures impact later-life phenotypes -- 1.2.2 Specific diets can influence outcomes in both the mother and offspring -- 1.3 Transmissibility of dietary effects to offspring -- 1.3.1 The adverse effects of maternal overnutrition on offspring -- 1.3.2 The effects of maternal undernutrition on offspring -- 1.4 Exploiting knowledge about maternal diet and epigenetics to improve parental and child health -- 1.4.1 Fatty acids in the maternal diet -- 1.4.2 Vitamins in the maternal diet -- 1.4.3 Other beneficial maternal diets -- 1.5 Implications and applications of dietary changes associated with epigenetics -- 1.5.1 Modifying in patients with cancer -- 1.5.2 Diet and systemic inflammation -- 1.5.3 Diet in age-related conditions and viral infections -- 1.5.4 Diet and personality -- 1.6 Plant dietary compounds in gastroenterological disorders -- 1.6.1 Curcumin -- 1.6.2 Flavonoids -- 1.7 Impact of diet on metabolic disease and diabetes -- 1.8 The impact of diet on carcinogenesis -- 1.9 The impact of diet on aging and aging-related disease -- 2 Conclusions -- References -- Section 5 Epigenetic alterations in organ specific diseases -- Chapter 12 Epigenetic regulations in neurological disorders -- 1 Introduction -- 2 Epigenetic modifications implicated in neurological disorders -- 2.1 DNA methylation -- 2.2 Histone modifications -- 2.3 Chromatin remodeling -- 2.4 Histone variants -- 2.5 Noncoding RNAs -- 3 Epigenetic links of neurodevelopmental disorders -- 3.1 Rett syndrome -- 3.2 Attention-deficit hyperactivity disorder -- 3.3 Autism spectrum disorder -- 4 Psychological disorders with epigenetic link -- 4.1 Fragile X syndrome -- 4.2 Schizophrenia -- 4.3 Bipolar disorder -- 4.4 Depression -- 4.5 Anxiety disorders. , 4.6 Epilepsy.