RNA-Based Regulation in Human Health and Disease (Volume 19) (Translational Epigenetics, Volume 19)

RNA-based Regulation in Human Health and Disease offers an in-depth exploration of RNA mediated genome regulation at different hierarchies. Beginning with multitude of canonical and non-canonical RNA populations, especially noncoding RNA in human physiology and evolution, further sections examine the various classes of RNAs (from small to large noncoding and extracellular RNAs), functional categories of RNA regulation (RNA-binding proteins, alternative splicing, RNA editing, antisense transcripts and RNA G-quadruplexes), dynamic aspects of RNA regulation modulating physiological homeostasis (aging), role of RNA beyond humans, tools and technologies for RNA research (wet lab and computational) and future prospects for RNA-based diagnostics and therapeutics. One of the core strengths of the book includes spectrum of disease-specific chapters from experts in the field highlighting RNA-based regulation in metabolic & neurodegenerative disorders, cancer, inflammatory disease, viral and bacterial infections. We hope the book helps researchers, students and clinicians appreciate the role of RNA-based regulation in genome regulation, aiding the development of useful biomarkers for prognosis, diagnosis, and novel RNA-based therapeutics. Comprehensive information of non-canonical RNA-based genome regulation modulating human health and disease Defines RNA classes with special emphasis on unexplored world of noncoding RNA at different hierarchies Disease specific role of RNA - causal, prognostic, diagnostic and therapeutic Features contributions from leading experts in the field Front Cover Epigenetics of the Immune System Copyright Contents Contributors Preface Chapter 1: An introduction to immunology and epigenetics Development of immune cells Dynamics of the immune response Immunological memory Basic overview of epigenetic regulation Genome architecture at primary structure scale: Cis-regulation through DNA elements Genome architecture at secondary structure scale: Trans-regulation through chromatin packaging and nucleosome positioning Genome architecture at tertiary structure scale: Long-range chromatic interactions and gene regulation within chromatin ter ... Posttranscriptional regulation of RNA expression Posttranslational modifications: Chromatin remodeling complexes and histones Posttranslational modifications: Nonhistone proteins Advancing technology and use of interdisciplinary approaches References Chapter 2: Plant epigenetics and the `intelligent ́ priming system to combat biotic stress Introduction Plant DNA methylation De novo DNA methylation Maintenance DNA methylation Histone modifications RNA-associated silencing Epigenetics of plant microbe interactions Epigenetics of plant insect interactions Epigenetics of immune system and memory in plants Plant epigenetics: Model plants and application in agriculture Somatic embryogenesis Heterosis Conclusions References Chapter 3: Understanding immune system development: An epigenetic perspective Introduction: An outline of the chapter Epigenetic modifications and their functional output Transcriptional control of epigenetic modifications: From on/off to cycling of epigenetic modifications DNA methylation: The mark of silence Histone modifications: Key epigenetic drivers Interdependence of DNA and histone modifications Epigenetic modifications mediated by chromatin remodeling and noncoding RNA (ncRNA) Accessible chromatin: A prelude to transcription Poised state of a gene: Epigenetic modifications priming gene for activation Epigenetic mechanisms regulating immune cell development Epigenetic regulation during hematopoiesis Development of innate immune cells: Regulation by epigenetic processes Development of natural killer (NK) cells ILC2 cell development Development of macrophages Development of dendritic cells Transcription factors and epigenetic mechanisms involved in DC development Epigenetic mechanisms in adaptive immune system B-cell development and differentiation-An epigenetic perspective Pro-B to pre-B cell commitment Pre-B to immature B cells-Formation of BCR Peripheral differentiation of B cells Role of epigenetic regulation in T cells From CLPs to T cells-Regulation by transcription factors and epigenetic modifications CD4/CD8 lineage commitment: The epigenetic contribution Terminal differentiation and function of T cells in the periphery Epigenetic changes in T-cell plasticity and memory Gene regulation by long-distance interactions Concluding remarks and future perspective Acknowledgments References Further reading Chapter 4: Epigenetic mechanisms in the regulation of lymphocyte differentiation Introduction Part I: Chromatin-based epigenetic mechanisms in lymphocyte differentiation DNA methylation and lineage commitment DNA methylation writers, readers, and erasers in immune cell differentiation Histone modifications in lymphocyte differentiation Histone modification writers, readers, and erasers in lymphocyte differentiation Chromatin accessibility in the differentiation of immune cells Part II: RNA-based mechanisms of regulation of lymphocyte differentiation MicroRNA-mediated regulation of T- and B-cell differentiation Specific miRNAs regulating T- and B-cell differentiation The emerging role of lncRNAs in immune cell differentiation LncRNAs in T-cell differentiation LncRNAs in B-cell differentiation Cross talk between noncoding RNAs Concluding remarks References Further reading Chapter 5: Epigenetics mechanisms driving immune memory cell differentiation and function Introduction Functional heterogeneity within the memory T-cell pool Histone methylation and pattern, acquisition of function DNA methylation and its role in regulating gene transcription Making sense of the ``junk DNA ́ ́: Noncoding regulatory elements work via chromatin folding Epigenetic regulation in the acquisition of lineage-specific T-cell function Epigenetic regulation in the acquisition of CD8 T-cell function Epigenetic mapping of the differentiation pathway that leads to T-cell memory The role of CD8+ T-cell-specific transcription factors in chromatin remodeling and acquisition of function Active regulation of chromatin state is a key factor in CD8+ T-cell effector vs memory fate decisions Conclusion References Chapter 6: Microbiota in the context of epigenetics of the immune system Introduction Epigenetic mechanisms Gut microbiome and epigenetics of immune cells Gut microbiota and epigenetics of Treg cells Gut microbiota and epigenetics of mononuclear phagocytes Gut microbiota and epigenetics of ILCs Gut microbiota and iNKT cells Skin microbiota and epigenetics of immune cells Microbiome and epigenetics of nonmucosal immune cells Microbiota and nonmucosal myeloid cells The case of SCFA The case of folate Epigenetic imprint of microbes on offspring's immune cells Conclusions and prospects References Chapter 7: Sequencing technologies for epigenetics: From basics to applications Introduction to high-throughput sequencing Next-generation sequencing Illumina sequencing protocol Library preparation Flow cell preparation Sequencing by synthesis Third-generation sequencing Nanopore sequencing SMRT sequencing Applications of sequencing technologies for epigenetics DNA methylation Histone modifications Other applications Data processing and computational analysis Raw data and quality control Read alignment Analysis of methylation data DNA methylation scoring Differential methylation Methylome segmentation Analysis of ChIP-seq data Quality control of ChIP-seq data Analysis of data from other applications Future perspectives References Chapter 8: Advances in single-cell epigenomics of the immune system Introduction Single-cell epigenomics technologies DNA modifications Protein-DNA interaction Chromatin structure Chromosome conformation Single-cell multiomics Computational challenges and solutions Quality control and preprocessing Downstream analysis Studying the immune system using single-cell epigenomics Hematopoiesis Leukemia Aging Conclusions and future perspectives Single-cell epigenomics with a spatial resolution Other future applications References Chapter 9: Machine learning and deep learning for the advancement of epigenomics The ``epigenetic code ́ ́ problem Progress of machine learning: Classification versus non-supervised learninga Unsupervised approaches Supervised approaches Methods for training data generation Classical classification methods Prediction of enhancer regulatory state with Bayesian networks Multiple kernel learning approach for the identification of tissue specific developmental enhancers Prediction of active enhancers based on DNA methylation marks and histone modifications with random forest classifier New approaches-Deep learning Conclusion Acknowledgments References Chapter 10: Systems immunology meets epigenetics Epigenetic modifications within the immune system DNA methylation RNA modification Histone modifications Systems approach for deconvoluting immune cell composition Deconvolution frameworks Reference-based models Reference-free models Perspectives References Chapter 11: Epigenetic deregulation of immune cells in autoimmune and autoinflammatory diseases Relevance of epigenetics for immune deregulation in autoimmune/autoinflammatory disorders Epigenetic dysregulation in autoimmune diseases Epigenetic defects of immune cells in rheumatoid arthritis Epigenetic defects of immune cells in psoriasis Epigenetic dysregulation in autoinflammatory diseases Familial Mediterranean fever Cryopyrin-associated periodic syndromes Epigenetic biomarkers in autoimmunity Targeting epigenetic defects References Chapter 12: Epigenetics of allergies: From birth to childhood Neonatal DNA methylation profiles as predictors of the trajectory to asthma and allergy DNA methylation profiles in patients with childhood asthma and allergy DNA methylation in the airways What have we learned so far? References Chapter 13: Epigenetic regulation of normal hematopoiesis and its dysregulation in hematopoietic malignancies Epigenetic regulation of normal hematopoiesis Epigenetic modifications Cis-regulatory elements Normal hematopoiesis Epigenome dynamics during normal hematopoietic differentiation Mutations of epigenetic regulators in clonal hematopoiesis and in hematopoietic neoplasms Preleukemic mutations Mutations in myeloid neoplasms Epigenetic deregulation in T-cell acute lymphoblastic leukemia Leukemogenesis of T-ALL Alterations in epigenetic modifiers Methylation profiles in T-ALL Deregulation of the TAL1 oncogene: A model for enhancer hijacking and oncogenic neo-enhancers Oncogenic neo-enhancers deregulating T-ALL oncogenes Cell-of-origin identification using epigenetics: Chronic lymphocytic leukemia as a model Epigenetically deregulated genes as biomarkers in CLL Methylomics identify CLL subgroups of different cellular origins Identification of disease-specific DNA methylation patterns in CLL Epigenomics for disease classification and as a diagnostic tool Epigenetic biomarkers DNA methylation biomarkers for cancer classification and risk assessment Computational models for cancer classification Epigenetic therapies in hematopoietic neoplasms Inhibitors of epigenetic key players Mechanisms of epigenetic therapies and possible rationales for drug combinations Acknowledgments References Chapter 14: Impact of epigenetic modifiers on the immune system Overview Epigenetic modifiers HDAC inhibitors HAT inhibitors DNMT inhibitors BET inhibitors EZH2 inhibitors LSD1 inhibitors DOT1L inhibitors Immunomodulatory effects of epigenetic modifiers Effect of HDACi on immune cells T cells Regulatory T (Treg) cells B cells Myeloid-derived suppressor cells Antigen-presenting cells Macrophages Dendritic cells Effect of DNMTi on immune cells T cells Treg cells B cells Macrophages Dendritic cells Clinical significance of epigenetic modifiers HDACi therapy DNMTi therapy Other epigenetic modifiers in therapy Combination therapy involving epigenetic modifiers Epigenetic modifiers and immunotherapy Epigenetic modifiers and chemotherapeutics Epigenetic modifiers and radiotherapy Combination therapy with HDACi and DNMTi Conclusion Acknowledgments Conflict of interest References Index Back Cover Rna-based Regulation In Human Health And Disease Offers An In-depth Exploration Of Rna Mediated Genome Regulation And Its Impact On Human Health And Disease. Beginning With A Fundamental Discussion Of Rna Biology In Human Physiology And Evolution, Further Sections Examine The Various Classes Of Rnas (from Small To Large Noncoding And Circulating Rnas), Functional Categories Of Rna Regulation (e.g. Alternative Splicing, A-i Editing, Antisense Transcripts, Rna G-quadruplexes, Crispr-cas9 And Riboswitches), Dynamic Aspects Of Rna Regulation (e.g., Rna Aggregates In Disease, Rna Toxicity, And Therapeutic Usage Of Rna Aptamers), Rna And Physiological Homeostasis, Tools And Technologies For Disease-focused Rna Research (e.g, Ngs Methods, Single Cell Omics), And Future Prospects For Rna-based Diagnostics And Treatments. Additionally, A Broad Range Of Disease-specific Chapters From Experts In The Field Detail Rna-based Regulation In Metabolic Disorders, Neurodegenerative Disorders, Cancer, Inflammatory Disease, Viral Infections, Bacterial Infections, And Stress Response. This Book Will Help Researchers, Students, And Clinicians Better Understand The Role Of Rna Regulation In Gene Expression, Aiding The Development Of Useful Biomarkers For Prognosis, Diagnosis, And New Rna-based Disease Therapies Provides A Comprehensive Analysis Of Rna Gene Expression Regulation Implicated In Human Health And Disease Thoroughly Defines Rna Classes; Functional Categories Of Rna Regulation; Dynamic Aspects Of Rna Regulation; Rna And Human Homeostasis; Use Of Non-human Rna In Therapeutics; Tools And Technologies For Disease-focused Rna Research; And Future Prospects For Rna-based Prognosis, Diagnostics, And Treatments Addresses Rna Regulation In Metabolic And Neurodegenerative Disorders, Cancer, Inflammatory Disease, Infection, And Stress Response Among Other Disorders And Physiological Processes Features Contributions From Leading Experts In The Field Rajesh Pandey's lab focuses on Integrative Genomics of Host-Pathogen wherein RNA plays a central role towards modulating pathogenicity. RNA-Based Regulation in Human Health and Disease offers an in-depth exploration of RNA-mediated genome regulation at different hierarchies. Beginning with a multitude of canonical and noncanonical RNA populations, especially noncoding RNA in human physiology and evolution, further sections examine the various classes of RNAs (from small to large noncoding and extracellular RNAs), functional categories of RNA regulation (RNA-binding proteins, alternative splicing, RNA editing, antisense transcripts, and RNA G-quadruplexes), dynamic aspects of RNA regulation modulating physiological homeostasis (aging), role of RNA beyond humans, tools and technologies for RNA research (wet lab and computational), and future prospects for RNA-based diagnostics and therapeutics. One of the core strengths of the book includes spectrum of disease-specific chapters from experts in the field highlighting RNA-based regulation in metabolic and neurodegenerative disorders, cancer, inflammatory disease, viral and bacterial infections. We hope the book helps researchers, students, and clinicians appreciate the role of RNA-based regulation in genome regulation, aiding the development of useful biomarkers for prognosis, diagnosis, and novel RNA-based therapeutics. -- 4e de couverture Rajesh Pandey's lab focuses on Integrative Genomics of Host-Pathogen wherein RNA plays a central role towards modulating pathogenicity. RNA-Based Regulation in Human Health and Disease offers an in-depth exploration of RNA-mediated genome regulation at different hierarchies. Beginning with a multitude of canonical and noncanonical RNA populations, especially noncoding RNA in human physiology and evolution, further sections examine the various classes of RNAs (from small to large noncoding and extracellular RNAs), functional categories of RNA regulation (RNA-binding proteins, alternative splicing, RNA editing, antisense transcripts, and RNA G-quadruplexes), dynamic aspects of RNA regulation modulating physiological homeostasis (aging), role of RNA beyond humans, tools and technologies for RNA research (wet lab and computational), and future prospects for RNA-based diagnostics and therapeutics. One of the core strengths of the book includes spectrum of disease-specific chapters from experts in the field highlighting RNA-based regulation in metabolic and neurodegenerative disorders, cancer, inflammatory disease, viral and bacterial infections. We hope the book helps researchers, students, and clinicians appreciate the role of RNA-based regulation in genome regulation, aiding the development of useful biomarkers for prognosis, diagnosis, and novel RNA-based therapeutics. -- Page 4 of cover