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Foreword; Preface; Reference; Contents; Abbreviations; 1: Epigenetic Regulation; 1.1 Introduction: Epigenetic Regulation in the Domains of Life; 1.2 Epigenetic Regulatory Mechanisms; 1.2.1 CpG Methylation; 1.2.2 Histone Modifications; 1.2.2.1 Histone Acetylation; 1.2.2.2 Histone Methylation; 1.2.2.3 Histone Phosphorylation; 1.2.2.4 Histone Ubiquitination; 1.2.2.5 Histone SUMOylation; 1.2.2.6 Histone ADP Ribosylation; 1.2.2.7 Histone Deimination; 1.2.2.8 Histone Proline Isomerization: A Noncovalent Histone Modification; 1.2.2.9 Histone O-GlcNAcylation
1.2.2.10 Histone Crotonylation1.2.3 Polycomb and Trithorax Complexes; 1.2.4 Variant Histones; 1.2.5 Pioneer Transcription Factors; 1.2.6 Long Noncoding RNAs; 1.2.7 Long-Distance Chromatin Interactions; 1.3 Chromatin Types; 1.3.1 Euchromatin (Active Chromatin); 1.3.2 Hererochromatin (Repressive Chromatin); 1.3.2.1 Polycomb-Repressed Chromatin; 1.3.2.2 Null Chromatin, Lamin- Associated Domains; 1.3.2.3 Constitutive Heterochromatin; 1.4 Coregulation of Gene Batteries; 1.4.1 Locus Control Regions, Chromatin Loops, Topologically Associated Domains; 1.4.2 Nuclear Subcompartments
1.4.3 Transcription Factories, Active Chromatin HubsReferences; 2: HIV-Induced Epigenetic Alterations in Host Cells; 2.1 Introduction; 2.2 Background on Epigenome; 2.3 HIV Integration; 2.4 HIV Latency and Reactivation; 2.5 HIV Progression and Epigenetic Modification; 2.6 Drugs Targeting Epigenetic Changes in HIV Infection; 2.7 Conclusion; References; 3: Epigenetic Alterations in Epstein-Barr Virus-Associated Diseases; 3.1 Introduction; 3.2 Physiological Course of EBV Infection; 3.3 EBV Latency Types and Tumors; 3.4 EBV Latency Gene Products
3.5 Establishing EBV Latency in Memory B Cells3.6 Epigenetic Regulation of EBV Latency Promoters; 3.7 Epigenetic Profiles of Cellular Genomes in EBV-Associated Neoplasms; 3.8 Conclusion; References; 4: Epigenetic Dysregulation in Virus-Associated Neoplasms; 4.1 Introduction: Oncoprotein-Mediated Epigenetic Reprogramming of Host Cells and Host Cell-Dependent Viral Epigenotypes; 4.2 Kaposi Sarcoma-Associated Herpesvirus (KSHV, Human Herpesvirus 8, HHV-8); 4.3 Hepatitis B Virus (HBV); 4.4 Hepatitis Delta Virus (HDV); 4.5 Hepatitis C Virus (HCV); 4.6 Human Papillomavirus (HPV)
4.7 Merkel Cell Polyomavirus (MCPyV)4.8 Human T-Cell Lymphotropic Virus Type I (HTLV-I); 4.9 Conclusion; References; 5: Epigenetic Alterations Induced by Bacterial Lipopolysaccharides; 5.1 Lipopolysaccharide Triggers Pro-inflammatory Response in Innate Immune Cells and Other Cell Types: An Overview; 5.2 Epigenetic Response to LPS during Inflammatory Process; 5.2.1 LPS-Induced Histone Modifications in Innate Immune Cells; 5.2.1.1 Histone Modifications at Inflammatory Genes after LPS Stimulation; 5.2.1.2 Use of HDAC Inhibitors to Study the LPS Response
1.2.2.10 Histone Crotonylation1.2.3 Polycomb and Trithorax Complexes; 1.2.4 Variant Histones; 1.2.5 Pioneer Transcription Factors; 1.2.6 Long Noncoding RNAs; 1.2.7 Long-Distance Chromatin Interactions; 1.3 Chromatin Types; 1.3.1 Euchromatin (Active Chromatin); 1.3.2 Hererochromatin (Repressive Chromatin); 1.3.2.1 Polycomb-Repressed Chromatin; 1.3.2.2 Null Chromatin, Lamin- Associated Domains; 1.3.2.3 Constitutive Heterochromatin; 1.4 Coregulation of Gene Batteries; 1.4.1 Locus Control Regions, Chromatin Loops, Topologically Associated Domains; 1.4.2 Nuclear Subcompartments
1.4.3 Transcription Factories, Active Chromatin HubsReferences; 2: HIV-Induced Epigenetic Alterations in Host Cells; 2.1 Introduction; 2.2 Background on Epigenome; 2.3 HIV Integration; 2.4 HIV Latency and Reactivation; 2.5 HIV Progression and Epigenetic Modification; 2.6 Drugs Targeting Epigenetic Changes in HIV Infection; 2.7 Conclusion; References; 3: Epigenetic Alterations in Epstein-Barr Virus-Associated Diseases; 3.1 Introduction; 3.2 Physiological Course of EBV Infection; 3.3 EBV Latency Types and Tumors; 3.4 EBV Latency Gene Products
3.5 Establishing EBV Latency in Memory B Cells3.6 Epigenetic Regulation of EBV Latency Promoters; 3.7 Epigenetic Profiles of Cellular Genomes in EBV-Associated Neoplasms; 3.8 Conclusion; References; 4: Epigenetic Dysregulation in Virus-Associated Neoplasms; 4.1 Introduction: Oncoprotein-Mediated Epigenetic Reprogramming of Host Cells and Host Cell-Dependent Viral Epigenotypes; 4.2 Kaposi Sarcoma-Associated Herpesvirus (KSHV, Human Herpesvirus 8, HHV-8); 4.3 Hepatitis B Virus (HBV); 4.4 Hepatitis Delta Virus (HDV); 4.5 Hepatitis C Virus (HCV); 4.6 Human Papillomavirus (HPV)
4.7 Merkel Cell Polyomavirus (MCPyV)4.8 Human T-Cell Lymphotropic Virus Type I (HTLV-I); 4.9 Conclusion; References; 5: Epigenetic Alterations Induced by Bacterial Lipopolysaccharides; 5.1 Lipopolysaccharide Triggers Pro-inflammatory Response in Innate Immune Cells and Other Cell Types: An Overview; 5.2 Epigenetic Response to LPS during Inflammatory Process; 5.2.1 LPS-Induced Histone Modifications in Innate Immune Cells; 5.2.1.1 Histone Modifications at Inflammatory Genes after LPS Stimulation; 5.2.1.2 Use of HDAC Inhibitors to Study the LPS Response