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Tet Proteins And Dna Demethylation
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Book Synopsis TET Proteins and DNA Demethylation by : Ozren Bogdanovic
Download or read book TET Proteins and DNA Demethylation written by Ozren Bogdanovic and published by Humana. This book was released on 2022-06-03 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the latest methods used to study various aspects of TET proteins and their biology. Chapters in this book are divided into five parts. Part One describes technologies aimed at detecting and quantifying DNA methylation turnover using massively parallel sequencing, ELISA, and mass spectrometry approaches. Part Two looks at data analyses protocols for distinguishing acting versus passive DNA demethylation and estimation of 5mC and 5hmC levels. Part Three deals with a new topic that takes advantage of modified CRISPR/Cas9 genome editing systems to target DNA demethylation activity to genomic loci of interest. Part Four discusses protocols that detail how to purify TET proteins and unravel their protein interactions, and Part Five looks at the assessment of TET protein function and activity in vivo and in vitro. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, TET Proteins and DNA Demethylation: Methods and Protocols is a valuable resource that aims to help research scientists at all levels working in the fields of DNA demethylation dynamics. Chapters 3, 7 and 17 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Book Synopsis TET Proteins and DNA Demethylation by : Ozren Bogdanovic
Download or read book TET Proteins and DNA Demethylation written by Ozren Bogdanovic and published by Humana. This book was released on 2021-05-20 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the latest methods used to study various aspects of TET proteins and their biology. Chapters in this book are divided into five parts. Part One describes technologies aimed at detecting and quantifying DNA methylation turnover using massively parallel sequencing, ELISA, and mass spectrometry approaches. Part Two looks at data analyses protocols for distinguishing acting versus passive DNA demethylation and estimation of 5mC and 5hmC levels. Part Three deals with a new topic that takes advantage of modified CRISPR/Cas9 genome editing systems to target DNA demethylation activity to genomic loci of interest. Part Four discusses protocols that detail how to purify TET proteins and unravel their protein interactions, and Part Five looks at the assessment of TET protein function and activity in vivo and in vitro. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, TET Proteins and DNA Demethylation: Methods and Protocols is a valuable resource that aims to help research scientists at all levels working in the fields of DNA demethylation dynamics. Chapters 3, 7 and 17 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Book Synopsis Epigenetic Therapy of Cancer by : Michael Lübbert
Download or read book Epigenetic Therapy of Cancer written by Michael Lübbert and published by Springer Science & Business Media. This book was released on 2013-12-12 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: The growing knowledge about disturbances of epigenetic gene regulation in hematopoietic stem cell disorders is now being translated into treatment approaches that target the epigenetic defects pharmacologically. This book first presents the latest evidence regarding the epigenetic regulation of hematopoietic stem cell differentiation and hemoglobin production. The significance of DNA methylation abnormalities in hematopoietic disorders and of epigenetic disturbances in lung cancer and other solid tumors is then discussed. A major part of the book, however, relates specifically to the translation of basic research and drug development to clinical applications, and in this context both present and future clinical strategies are considered. Individual chapters are devoted to the use of DNA hypomethylating agents and chromatin-modifying agents, and the treatment of hematologic malignancies and solid tumors by means of epigenetic agents is discussed in detail.
Book Synopsis Role of TET Proteins in B Cells and Treg Cells by : Daniela Samaniego Castruita
Download or read book Role of TET Proteins in B Cells and Treg Cells written by Daniela Samaniego Castruita and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA demethylation is promoted by TET enzymes, a family of three proteins--TET1, TET2 and TET3--which oxidize methyl group of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). TET proteins have been previously associated to cancer. In particular, Tet2 loss of function is strongly associated to haematopoietic malignancies in humans, such as B cell and T cell lymphoma. In this dissertation we explore the role of TET proteins in B and Treg cells. To do this we rely in the use of in vivo and in vitro models. We generated a mouse model with Tet2/3 deletion, CD19 Tet2/3 DKO mice. The TET deficient mice showed an expansion of Germinal Center B cells and developed B cell lymphoma, as early as 6 weeks of age; coupled to this, we observed an increase of G-quaruplexes and R-loops and increase of DNA damage. Mice generated with the adiddtional [additional] deletion of DNMT1, the enzyme responsible to maintain DNA methylation and also a G-quadruplex binding protein, on top of the Tet2/3 deletion, showed an inhibition of Germinal Center B cells and a significant delay on B cell lymphoma. We also explored the role of TET proteins in Treg cells using genomic and epigenomic approaches in in vivo and in vitro models. The Tet2/3 deficient Treg cells showed a loss of Treg-specific molecular features, and an impairement of IL-2/STAT5 signaling pathway. In our in vitro system, we induced Treg (iTreg) cells with TGF[beta] and treated them with Vitamin C, a potent activator of TET proteins and other dioxygenases. Oposite [opposite] to what we observed in vivo, boosting TET activity with Vitamin C enhanced IL-2 responsiveness in iTreg cells by increasing IL2R[alpha] expression and STAT5 activity.
Book Synopsis DNA Methyltransferases - Role and Function by : Albert Jeltsch
Download or read book DNA Methyltransferases - Role and Function written by Albert Jeltsch and published by Springer. This book was released on 2016-11-08 with total page 537 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA methyltransferases are important enzymes in a broad range of organisms. Dysfunction of DNA methyltransferases in humans leads to many severe diseases, including cancer. This book focuses on the biochemical properties of these enzymes, describing their structures and mechanisms in bacteria, humans and other species, including plants, and also explains the biological processes of reading of DNA methylation and DNA demethylation. It covers many emerging aspects of the biological roles of DNA methylation functioning as an essential epigenetic mark and describes the role of DNA methylation in diseases. Moreover, the book explains modern technologies, like targeted rewriting of DNA methylation by designed DNA methyltransferases, as well as technological applications of DNA methyltransferases in DNA labelling. Finally, the book summarizes recent methods for the analysis of DNA methylation in human DNA. Overall, this book represents a comprehensive state-of-the-art- work and is a must-have for advanced researchers in the field of DNA methylation and epigenetics.
Book Synopsis Stress: Genetics, Epigenetics and Genomics by : George Fink
Download or read book Stress: Genetics, Epigenetics and Genomics written by George Fink and published by Academic Press. This book was released on 2020-10-24 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: This fourth volume in the Handbook of Stress series, Stress: Genetics, Epigenetics and Genomics, deals with the influence that genetics, epigenetics, and genomics have on the effects of and responses to stress. Chapters refer to epigenetic mechanisms that involve DNA methylation, histone modification, and/or noncoding RNA-associated gene activation or silencing. There is also coverage of epigenetic mechanisms in stress-related transgenerational transmission of characteristics, and how these may help explain heritability in some complex human diseases.The Handbook of Stress series, comprised of self-contained volumes that each focus on a specific stress area, covers the significant advances made since the publication of Elsevier’s Encyclopedia of Stress (2000 and 2007). Volume 4 is ideal for graduate students, post-doctoral fellows, faculty and clinicians interested in stress genetics, epigenetics and genomics involved in neuroendocrinology, neuroscience, biomedicine, endocrinology, psychology, psychiatry and the social sciences Articles carefully selected by eminent stress researchers and prepared by contributors representing outstanding scholarship in the field, with each chapter fully vetted for reliable expert knowledge Richly illustrated with explanatory figures and tables Each chapter includes a boxed “Key points call out section Affordably priced, self-contained volume for readers specifically interested in stress genetics and epigenetics, removing the need to purchase the whole Handbook series
Book Synopsis Introduction to Epigenetics by : Renato Paro
Download or read book Introduction to Epigenetics written by Renato Paro and published by Springer Nature. This book was released on 2021-03-23 with total page 215 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access textbook leads the reader from basic concepts of chromatin structure and function and RNA mechanisms to the understanding of epigenetics, imprinting, regeneration and reprogramming. The textbook treats epigenetic phenomena in animals, as well as plants. Written by four internationally known experts and senior lecturers in this field, it provides a valuable tool for Master- and PhD- students who need to comprehend the principles of epigenetics, or wish to gain a deeper knowledge in this field. After reading this book, the student will: Have an understanding of the basic toolbox of epigenetic regulation Know how genetic and epigenetic information layers are interconnected Be able to explain complex epigenetic phenomena by understanding the structures and principles of the underlying molecular mechanisms Understand how misregulated epigenetic mechanisms can lead to disease
Book Synopsis Environmental Epigenetics by : L. Joseph Su
Download or read book Environmental Epigenetics written by L. Joseph Su and published by Springer. This book was released on 2015-05-18 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book examines the toxicological and health implications of environmental epigenetics and provides knowledge through an interdisciplinary approach. Included in this volume are chapters outlining various environmental risk factors such as phthalates and dietary components, life states such as pregnancy and ageing, hormonal and metabolic considerations and specific disease risks such as cancer cardiovascular diseases and other non-communicable diseases. Environmental Epigenetics imparts integrative knowledge of the science of epigenetics and the issues raised in environmental epidemiology. This book is intended to serve both as a reference compendium on environmental epigenetics for scientists in academia, industry and laboratories and as a textbook for graduate level environmental health courses. Environmental Epigenetics imparts integrative knowledge of the science of epigenetics and the issues raised in environmental epidemiology. This book is intended to serve both as a reference compendium on environmental epigenetics for scientists in academia, industry and laboratories and as a textbook for graduate level environmental health courses.
Book Synopsis Dynamic regulation of DNA methylation in human T-cell biology by : Antonio Lentini
Download or read book Dynamic regulation of DNA methylation in human T-cell biology written by Antonio Lentini and published by Linköping University Electronic Press. This book was released on 2019-03-19 with total page 65 pages. Available in PDF, EPUB and Kindle. Book excerpt: T helper cells play a central role in orchestrating immune responses in humans. Upon encountering a foreign antigen, T helper cells are activated followed by a differentiation process where the cells are specialised to help combating the infection. Dysregulation of T helper cell activation, differentiation and function has been implicated in numerous diseases, including autoimmunity and cancer. Whereas gene-regulatory networks help drive T-cell differentiation, acquisition of stable cell states require heritable epigenetic signals, such as DNA methylation. Indeed, the establishment of DNA methylation patterns is a key part of appropriate T-cell differentiation but how this is regulated over time remains unknown. Methylation can be directly attached to cytosine residues in DNA to form 5-methylcytosine (5mC) but the removal of DNA methylation requires multiple enzymatic reactions, commonly initiated by the conversion into 5-hydroxymethylcytosine (5hmC), thus creating a highly complex regulatory system. This thesis aimed to investigate how DNA methylation is dynamically regulated during T-cell differentiation. To this end, we employed large-scale profiling techniques combining gene expression as well as genome-wide 5mC and 5hmC measurements to construct a time-series model of epigenetic regulation of differentiation. This revealed that early T-cell activation was accompanied by extensive genome-wide deposition of 5hmC which resulted in demethylation upon proliferation. Early DNA methylation remodelling through 5hmC was not only indicative of demethylation events during T-cell differentiation but also marked changes persisting longterm in memory T-cell subsets. These results suggest that priming of epigenetic landscapes in T-cells is initiated during early activation events, preceding any establishment of a stable lineage, which are then maintained throughout the cells lifespan. The regions undergoing remodelling were also highly enriched for genetic variants in autoimmune diseases which we show to be functional through disruption of protein binding. These variants could potentially disrupt gene-regulatory networks and the establishment of epigenetic priming, highlighting the complex interplay between genetic and epigenetic layers. In the course of this work, we discovered that a commonly used technique to study genome-wide DNA modifications, DNA immunoprecipitation (DIP)-seq, had a false discovery rate between 50-99% depending on the modification and cell type being assayed. This represented inherent technical errors related to the use of antibodies resulting in off-target binding of repetitive sequences lacking any DNA modifications. These sequences are common in mammalian genomes making robust detection of rare DNA modifications very difficult due to the high background signals. However, offtarget binding could easily be controlled for using a non-specific antibody control which greatly improved data quality and biological insight of the data. Although future studies are advised to use alternative methods where available, error correction is an acceptable alternative which will help fuel new discoveries through the removal of extensive background signals. Taken together, this thesis shows how integrative use of high-resolution epigenomic data can be used to study complex biological systems over time as well as how these techniques can be systematically characterised to identify and correct errors resulting in improved detection.
Book Synopsis Epigenetics of Aging by : Trygve O. Tollefsbol
Download or read book Epigenetics of Aging written by Trygve O. Tollefsbol and published by Springer Science & Business Media. This book was released on 2009-11-11 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent studies have indicated that epigenetic processes may play a major role in both cellular and organismal aging. These epigenetic processes include not only DNA methylation and histone modifications, but also extend to many other epigenetic mediators such as the polycomb group proteins, chromosomal position effects, and noncoding RNA. The topics of this book range from fundamental changes in DNA methylation in aging to the most recent research on intervention into epigenetic modifications to modulate the aging process. The major topics of epigenetics and aging covered in this book are: 1) DNA methylation and histone modifications in aging; 2) Other epigenetic processes and aging; 3) Impact of epigenetics on aging; 4) Epigenetics of age-related diseases; 5) Epigenetic interventions and aging: and 6) Future directions in epigenetic aging research. The most studied of epigenetic processes, DNA methylation, has been associated with cellular aging and aging of organisms for many years. It is now apparent that both global and gene-specific alterations occur not only in DNA methylation during aging, but also in several histone alterations. Many epigenetic alterations can have an impact on aging processes such as stem cell aging, control of telomerase, modifications of telomeres, and epigenetic drift can impact the aging process as evident in the recent studies of aging monozygotic twins. Numerous age-related diseases are affected by epigenetic mechanisms. For example, recent studies have shown that DNA methylation is altered in Alzheimer’s disease and autoimmunity. Other prevalent diseases that have been associated with age-related epigenetic changes include cancer and diabetes. Paternal age and epigenetic changes appear to have an effect on schizophrenia and epigenetic silencing has been associated with several of the progeroid syndromes of premature aging. Moreover, the impact of dietary or drug intervention into epigenetic processes as they affect normal aging or age-related diseases is becoming increasingly feasible.
Book Synopsis Association of TET Loss of Function with Heterochromatin DNA Hypomethylation and Genome Instability by : Isaac Fernando López Moyado
Download or read book Association of TET Loss of Function with Heterochromatin DNA Hypomethylation and Genome Instability written by Isaac Fernando López Moyado and published by . This book was released on 2019 with total page 122 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cancer genomes are characterized by focal increases in DNA methylation, co-occurring with widespread hypomethylation. Here we show that TET loss-of-function results in a similar genomic footprint. Both 5hmC in wildtype genomes, and DNA hypermethylation in TET-deficient genomes, are largely confined to the active euchromatic compartment, consistent with the known functions of TET proteins in DNA demethylation and the known distribution of 5hmC at transcribed genes and active enhancers. In contrast, an unexpected DNA hypomethylation noted in multiple TET-deficient genomes is primarily observed in the heterochromatin compartment. In a mouse model of T cell lymphoma driven by TET deficiency (Tet2/3 DKO T cells), genomic analysis of malignant T cells revealed DNA hypomethylation in the heterochromatic genomic compartment, as well as reactivation of repeat elements and enrichment for single nucleotide alterations, primarily in heterochromatic regions of the genome. Furthermore, like DNMT-deficient cells, expanded Tet2/3 DKO T cells displayed recurrent aneuploidies and increased accumulation of DNA double-strand breaks. Noteworthy, hematopoietic stem/precursor cells (HSPC) doubly deficient for Tet2 and Dnmt3a displayed greater losses of DNA methylation than HSPC singly deficient for Tet2 or Dnmt3a alone, potentially explaining the unexpected synergy between DNMT3A and TET2 mutations in myeloid and lymphoid malignancies. Tet1-deficient cells showed decreased localization of Dnmt3a in the heterochromatin compartment compared to WT cells, pointing to a functional interaction between TET and DNMT proteins and providing a potential explanation for the hypomethylation observed in TET-deficient genomes. Our data suggest that TET loss-of-function may at least partially underlie the characteristic pattern of global hypomethylation coupled to regional hypermethylation observed in diverse cancer genomes, propose that heterochromatin DNA hypomethylation may at least partially explain some of the shared features between TET and DNMT mutants, and highlight the potential contribution of heterochromatin hypomethylation to oncogenesis.
Book Synopsis Gadd45 Stress Sensor Genes by : Dan A. Liebermann
Download or read book Gadd45 Stress Sensor Genes written by Dan A. Liebermann and published by Springer Science & Business Media. This book was released on 2013-10-08 with total page 141 pages. Available in PDF, EPUB and Kindle. Book excerpt: Emerging evidence indicates that the Gadd45 family of genes play a unique and critical role as sensors of stress, including genotoxic, physiological and oncogenic stress. The stress response Gadd45 family of genes (Gadd45a, Gadd45b & Gadd45g), discovered by Dr. Liebermann and other researchers, encode for small (18 kd) nuclear/cytoplasmic proteins). These genes are rapidly induced by a wide variety of endogenous and exogenous stress stimuli. In spite of marked similarities, Gadd45 genes are regulated differently & exhibit functional diversity. Gadd45 are implicated in cell cycle arrest, DNA demethylation & repair, apoptosis, cell survival, genomic stability, inflammation, & in response to physiological and oncogenic stress. Functions of Gadd45 genes are mediated by protein-protein interactions that modulate structure/function of other cellular proteins implicated in cell cycle regulation and the response of cells to stress; these interactions vary depending upon the biological setting including cell type, developmental stage and stress/stimulus. Protein partners include cdc2/cyclinB1, p21, the p38/JNK stress induced kinase pathways, and PCNA/histones. The purpose of this book is to provide a comprehensive picture of the unique global role Gadd45 genes play as stress sensors & the molecular pathways involved.
Book Synopsis DNA Methylation and Complex Human Disease by : Michel Neidhart
Download or read book DNA Methylation and Complex Human Disease written by Michel Neidhart and published by Academic Press. This book was released on 2015-08-11 with total page 546 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA Methylation and Complex Human Disease reviews the possibilities of methyl-group-based epigenetic biomarkers of major diseases, tailored epigenetic therapies, and the future uses of high-throughput methylome technologies. This volume includes many pertinent advances in disease-bearing research, including obesity, type II diabetes, schizophrenia, and autoimmunity. DNA methylation is also discussed as a plasma and serum test for non-invasive screening, diagnostic and prognostic tests, as compared to biopsy-driven gene expression analysis, factors which have led to the use of DNA methylation as a potential tool for determining cancer risk, and diagnosis between benign and malignant disease. Therapies are at the heart of this volume and the possibilities of DNA demethylation. In cancer, unlike genetic mutations, DNA methylation and histone modifications are reversible and thus have shown great potential in the race for effective treatments. In addition, the authors present the importance of high-throughput methylome analysis, not only in cancer, but also in non-neoplastic diseases such as rheumatoid arthritis. Discusses breaking biomarker research in major disease families of current health concern and research interest, including obesity, type II diabetes, schizophrenia, and autoimmunity Summarizes advances not only relevant to cancer, but also in non-neoplastic disease, currently an emerging field Describes wholly new concepts, including the linking of metabolic pathways with epigenetics Provides translational researchers with the knowledge of both basic research and clinic applications of DNA methylation in human diseases
Book Synopsis Epigenetic Regulation in the Nervous System by : Junjie U. Guo
Download or read book Epigenetic Regulation in the Nervous System written by Junjie U. Guo and published by Elsevier Inc. Chapters. This book was released on 2012-12-31 with total page 31 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis DNA Methylation of Endothelial Cell-enriched Genes During in Vitro Mouse ES Cell Differentiation and the Role of TET Proteins by : Olga Vexelshtein
Download or read book DNA Methylation of Endothelial Cell-enriched Genes During in Vitro Mouse ES Cell Differentiation and the Role of TET Proteins written by Olga Vexelshtein and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Bioinformatics in Aquaculture by : Zhanjiang (John) Liu
Download or read book Bioinformatics in Aquaculture written by Zhanjiang (John) Liu and published by John Wiley & Sons. This book was released on 2017-04-17 with total page 605 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics derives knowledge from computer analysis of biological data. In particular, genomic and transcriptomic datasets are processed, analysed and, whenever possible, associated with experimental results from various sources, to draw structural, organizational, and functional information relevant to biology. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics in Aquaculture provides the most up to date reviews of next generation sequencing technologies, their applications in aquaculture, and principles and methodologies for the analysis of genomic and transcriptomic large datasets using bioinformatic methods, algorithm, and databases. The book is unique in providing guidance for the best software packages suitable for various analysis, providing detailed examples of using bioinformatic software and command lines in the context of real world experiments. This book is a vital tool for all those working in genomics, molecular biology, biochemistry and genetics related to aquaculture, and computational and biological sciences.
Download or read book Pharmacoepigenetics written by and published by Academic Press. This book was released on 2019-06-04 with total page 983 pages. Available in PDF, EPUB and Kindle. Book excerpt: Pharmacoepigenetics, Volume Eleven provides a comprehensive volume on the role of epigenetics and epigenomics in drug discovery and development, providing a detailed, but accessible, view of the field, from basic principles, to applications in disease therapeutics. Leading international researchers from across academia, clinical settings and the pharmaceutical industry discuss the influence of epigenetics and epigenomics in human pathology, epigenetic biomarkers for disease prediction, diagnosis, and treatment, current epigenetic drugs, and the application of epigenetic procedures in drug development. Throughout the book, chapter authors offer a balanced and objective discussion of the future of pharmacoepigenetics and its crucial contribution to the growth of precision and personalized medicine. Fully examines the influence of epigenetics and epigenomics in human pathology, epigenetic biomarkers for disease prediction, diagnosis, treatment, current epigenetic drugs and the application of epigenetic procedures in drug development Features chapter contributions from leading international researchers in academia, clinical settings and the pharmaceutical industry Instructs researchers, students and clinicians on how to better interpret and employ pharmacoepigenetics in drug development, efficiency and safety Provides a balanced and objective discussion of the future of pharmacoepigenetics and its crucial role in precision medicine
