Epigenetic Gene Expression and Regulation

Epigenetic Gene Expression and Regulation PDF Author: Suming Huang
Publisher: Academic Press
ISBN: 0128004711
Category : Science
Languages : en
Pages : 482

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Book Description
Epigenetic Gene Expression and Regulation reviews current knowledge on the heritable molecular mechanisms that regulate gene expression, contribute to disease susceptibility, and point to potential treatment in future therapies. The book shows how these heritable mechanisms allow individual cells to establish stable and unique patterns of gene expression that can be passed through cell divisions without DNA mutations, thereby establishing how different heritable patterns of gene regulation control cell differentiation and organogenesis, resulting in a distinct human organism with a variety of differing cellular functions and tissues. The work begins with basic biology, encompasses methods, cellular and tissue organization, topical issues in epigenetic evolution and environmental epigenesis, and lastly clinical disease discovery and treatment. Each highly illustrated chapter is organized to briefly summarize current research, provide appropriate pedagogical guidance, pertinent methods, relevant model organisms, and clinical examples. Reviews current knowledge on the heritable molecular mechanisms that regulate gene expression, contribute to disease susceptibility, and point to potential treatment in future therapies Helps readers understand how epigenetic marks are targeted, and to what extent transgenerational epigenetic changes are instilled and possibly passed onto offspring Chapters are replete with clinical examples to empower the basic biology with translational significance Offers more than 100 illustrations to distill key concepts and decipher complex science

Epigenetic Mechanisms of Gene Regulation

Epigenetic Mechanisms of Gene Regulation PDF Author: Vincenzo E. A. Russo
Publisher:
ISBN:
Category : Science
Languages : en
Pages : 692

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Book Description
Many inheritable changes in gene function are not explained by changes in the DNA sequence. Such epigenetic mechanisms are known to influence gene function in most complex organisms and include effects such as transposon function, chromosome imprinting, yeast mating type switching and telomeric silencing. In recent years, epigenetic effects have become a major focus of research activity. This monograph, edited by three well-known biologists from different specialties, is the first to review and synthesize what is known about these effects across all species, particularly from a molecular perspective, and will be of interest to everyone in the fields of molecular biology and genetics.

A Systems Biology Approach to Epigenetic Gene Regulation

A Systems Biology Approach to Epigenetic Gene Regulation PDF Author: Stephen Patrick Wilson
Publisher:
ISBN:
Category :
Languages : en
Pages : 262

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Book Description
The ability to control when, and how much of the genetic code is being expressed is the underlying principle behind gene regulation. Control of gene production is able to influence a cell's phenotype by determining which structural components of the cell's observable traits (shape, growth, and behavior) are made. In multicellular organism's different cell types are able to arise from the same genetic code due to a difference in the patterns of genes being expressed. Essentially anywhere in the process of gene expression from transcription, RNA processing, translation, and post-translational modifications of the protein is subject to regulation. As transcription is the first step in the process of gene expression, it is the first level of regulation for influencing the cell phenotype. The actions of transcription factors, histone modifiers, and other proteins work together to influence RNA polymerase's ability to complete the process of transcription. The actions of transcription factors are able to influence transcription by controlling the ability of RNA polymerase to be recruited to the start of a protein coding region and histone modifiers can rearrange the histones of the chromatin causing entire regions of a chromosome to become exposed or sequestered. These transcriptional regulators are able to work in a combinatorial fashion with one another to either activate and/or repress wide repertoires of transcriptional targets. Mapping out a network of interactions between these transcriptional regulators in gene expression programs allows researchers to understand how each protein is able to influence the phenotype of the cell, and how mutations to any of these transcriptional regulators are able to drive the cell into a diseased state. In the case of cancer, changes in the mechanisms of gene regulation brought on by mutations to these transcriptional regulators may drive the cell's hyper proliferative state. With the creation of next generation sequencing researchers are now better able to define where regulation is taking place in the genome, and how much it is able to influence gene expression. This gives researchers the ability to build these gene regulatory networks and evaluate their impact on gene expression. The subsequent chapters of this dissertation are a reflection of my published work investigating the contribution of oncogenic processes to gene regulatory networks in cancer through the study of hyperactivating somatic mutation of a histone modifier, changes in transcription factor response element specificity, epigenetic regulation of transcription factor signaling, and a transcription factor coactivation network.

Chromatin and Gene Regulation

Chromatin and Gene Regulation PDF Author: Bryan M. Turner
Publisher: John Wiley & Sons
ISBN: 0470751673
Category : Science
Languages : en
Pages : 288

Get Book

Book Description
Written in an informal and accessible style, Chromatin and Gene Regulation enables the reader to understand the science of this rapidly moving field. Chromatin is a fundamental component in the network of controls that regulates gene expression. Many human diseases have been linked to disruption of these control processes by genetic or environmental factors, and unravelling the mechanisms by which they operate is one of the most exciting and rapidly developing areas of modern biology. Chromatin is central both to the rapid changes in gene transcription by which cells respond to changes in their environment and also to the maintenance of gene expression patterns from one cell generation to the next. This book will be an invaluable guide to undergraduate and postgraduate students in the biological sciences and all those with an interest in the medical implications of aberrant gene expression.

Epigenetic Gene Regulation in Stem Cell Differentiation and Reprogramming

Epigenetic Gene Regulation in Stem Cell Differentiation and Reprogramming PDF Author: Kevin Huang
Publisher:
ISBN:
Category :
Languages : en
Pages : 223

Get Book

Book Description
The regulatory capacities of epigenetic mechanisms including DNA methylation, histone modifications, and non-coding RNAs, have seen a rising interest in recent years. These epigenetic marks are pervasive and non-randomly distributed across the genome, raising intriguing questions on how epigenetics contributes to genomic features that define cellular identity and function. Unlike fixed genetic information that is shared between all cell types, epigenetics involve multiple layers of regulation and can vary dramatically across different cell types and genomic contexts. Thus, much more effort is required to procure a complete perspective of the manifold epigenetic landscape. The body of work in this dissertation focuses on epigenetic studies in the mammalian pluripotent stem cell model system. We utilize high-throughput technologies such as microarrays and next-generation sequencing (NGS) as well as leverage existing epigenetic maps to address a wide range of molecular questions on a comprehensive global scale. This dissertation is organized into three overarching themes: First, we employed genome-wide gene expression and DNA methylation profiling tools to determine whether different cell types display unique biomarkers that can be used to distinguish them from other cell types (Chapters 2-5). We found that human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) carry distinct features in both gene expression and DNA methylation patterns, arguing in favor of the idea that these two pluripotent cell types are different. Furthermore, we compared pluripotent stem cell derived retinal pigmented epithelium (hESC-RPE and hiPSC-RPE) with fetal and adult RPE and found that all RPE cells share a core set of signature genes that distinguishes them from all other cell types. We propose these signature genes will be useful for evaluating the quality of stem-cell derived RPE. Finally, novel corneal endothelial cells (CECs) biomarkers were identified through comparing 12 other tissue types, paving the way for future studies to evaluate properties of stem-cell derived CECs. We next examined how molecular features of pluripotent stem cells are altered during the differentiation process of stem cells (Chapters 6-8). Using the RPE differentiation paradigm, we profiled both microRNA and DNA methylation patterns in intermediate stages between pluripotent stem cells and mature RPE. These two separate studies identified subsets of dynamically regulated epigenetic marks, some of which are associated with RPE signature gene expression. Furthermore, we used a highly innovative and powerful single-cell RNA-sequencing approach to profile transcriptional changes in the early embryo beginning from mature oocyte to morula stages. This study identified a conserved genetic program describing a highly dynamic transcriptional architecture during early embryogenesis. Finally, we took a focused analysis on how DNA methyltransferases contribute to shaping the pluripotent stem cell epigenome (Chapters 9-10). Using mouse ESCs null of DNA methylation, we determined DNA methylation regulates a large set of genes through action with H3K27me3. Furthermore, we determined shared and unique genomic targets of each DNA methyltransferase, including novel de novo methylation activity for Dnmt1 in vivo. In the human model system, we generated iPSCs from ICF Syndrome patient fibroblasts which carry double heterozygous mutations in DNMT3B. We found DNMT3B is involved in a wave of de novo methylation during the reprogramming process and has unique genomic targets.

Non-coding RNAs and Epigenetic Regulation of Gene Expression

Non-coding RNAs and Epigenetic Regulation of Gene Expression PDF Author: Kevin V. Morris
Publisher: Horizon Scientific Press
ISBN: 9781904455943
Category : Science
Languages : en
Pages : 216

Get Book

Book Description
Non-coding RNAs potentially play an active role in modulating gene transcription and epigenetic states. Several genes in differentiated cells may be under some form of RNA-based transcriptional and epigenetic regulatory control. This form of regulation may be controlled by selective pressures and influence the adaptability of the cell. The concept that RNA can control epigenetic states impacts our understanding of the basic fabric of the cell and may have therapeutic potential. Many studies have been carried out on the modulation of gene transcription by non-coding RNAs. This book, written by a group of distinguished scientists, represents an important overview and summary of the field to date. The 13 chapters are organized into three sections: a) Non-coding RNAs: Form, Function and Diversity; b) Non-coding RNAs: Gene Regulation and Epigenetics; and c) Non-coding RNAs: Disease and Therapeutics. This up-to-date volume is an essential book for those working in the area and represents a major information resource on current research in the fast-moving fields of epigenetics, the regulation of gene expression, and RNA research.

Recent Advances of Epigenetics in Crop Biotechnology

Recent Advances of Epigenetics in Crop Biotechnology PDF Author: Clelia De-la-Peña
Publisher: Frontiers Media SA
ISBN: 2889198545
Category :
Languages : en
Pages :

Get Book

Book Description
Epigenetics is a new field that explains gene expression at the chromatin structure and organization level. Three principal epigenetic mechanisms are known and hundreds of combinations among them can develop different phenotypic characteristics. DNA methylation, histone modifications and small RNAs have been identified, and their functions are being studied in order to understand the mechanisms of interaction and regulation among the different biological processes in plants. Although, fundamental epigenetic mechanisms in crop plants are beginning to be elucidated, the comprehension of the different epigenetic mechanisms, by which plant gene regulation and phenotype are modified, is a major topic to develop in the near future in order to increase crop productivity. Thus, the importance of epigenetics in improving crop productivity is undoubtedly growing. Current research on epigenetics suggest that DNA methylation, histone modifications and small RNAs are involved in almost every aspect of plant life including agronomically important traits such as flowering time, fruit development, responses to environmental factors, defense response and plant growth. The aim of this Research Topic is to explore the recent advances concerning the role of epigenetics in crop biotechnology, as well as to enhance and promote interactions among high quality researchers from different disciplines such as genetics, cell biology, pathology, microbiology, and evolutionary biology in order to join forces and decipher the epigenetic mechanisms in crop productivity.

Regulation of gene expression

Regulation of gene expression PDF Author: U Satyanarayana
Publisher: Elsevier Health Sciences
ISBN: 8131241831
Category : Medical
Languages : en
Pages : 21

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Book Description
Regulation of gene expression Regulation of gene expression

Long-Range Control of Gene Expression

Long-Range Control of Gene Expression PDF Author: Veronica van Heyningen
Publisher: Academic Press
ISBN: 9780080877815
Category : Science
Languages : en
Pages : 416

Get Book

Book Description
Long-Range Control of Gene Expression covers the current progress in understanding the mechanisms for genomic control of gene expression, which has grown considerably in the last few years as insight into genome organization and chromatin regulation has advanced. Discusses the evolution of cis-regulatory sequences in drosophila Includes information on genomic imprinting and imprinting defects in humans Includes a chapter on epigenetic gene regulation in cancer

Epigenetic Gene Expression and Regulation

Epigenetic Gene Expression and Regulation PDF Author: Suming Huang
Publisher: Academic Press
ISBN: 0128004711
Category : Science
Languages : en
Pages : 482

View

Book Description
Epigenetic Gene Expression and Regulation reviews current knowledge on the heritable molecular mechanisms that regulate gene expression, contribute to disease susceptibility, and point to potential treatment in future therapies. The book shows how these heritable mechanisms allow individual cells to establish stable and unique patterns of gene expression that can be passed through cell divisions without DNA mutations, thereby establishing how different heritable patterns of gene regulation control cell differentiation and organogenesis, resulting in a distinct human organism with a variety of differing cellular functions and tissues. The work begins with basic biology, encompasses methods, cellular and tissue organization, topical issues in epigenetic evolution and environmental epigenesis, and lastly clinical disease discovery and treatment. Each highly illustrated chapter is organized to briefly summarize current research, provide appropriate pedagogical guidance, pertinent methods, relevant model organisms, and clinical examples. Reviews current knowledge on the heritable molecular mechanisms that regulate gene expression, contribute to disease susceptibility, and point to potential treatment in future therapies Helps readers understand how epigenetic marks are targeted, and to what extent transgenerational epigenetic changes are instilled and possibly passed onto offspring Chapters are replete with clinical examples to empower the basic biology with translational significance Offers more than 100 illustrations to distill key concepts and decipher complex science

Epigenetic Mechanisms of Gene Regulation

Epigenetic Mechanisms of Gene Regulation PDF Author: Vincenzo E. A. Russo
Publisher:
ISBN:
Category : Science
Languages : en
Pages : 692

View

Book Description
Many inheritable changes in gene function are not explained by changes in the DNA sequence. Such epigenetic mechanisms are known to influence gene function in most complex organisms and include effects such as transposon function, chromosome imprinting, yeast mating type switching and telomeric silencing. In recent years, epigenetic effects have become a major focus of research activity. This monograph, edited by three well-known biologists from different specialties, is the first to review and synthesize what is known about these effects across all species, particularly from a molecular perspective, and will be of interest to everyone in the fields of molecular biology and genetics.

A Systems Biology Approach to Epigenetic Gene Regulation

A Systems Biology Approach to Epigenetic Gene Regulation PDF Author: Stephen Patrick Wilson
Publisher:
ISBN:
Category :
Languages : en
Pages : 262

View

Book Description
The ability to control when, and how much of the genetic code is being expressed is the underlying principle behind gene regulation. Control of gene production is able to influence a cell's phenotype by determining which structural components of the cell's observable traits (shape, growth, and behavior) are made. In multicellular organism's different cell types are able to arise from the same genetic code due to a difference in the patterns of genes being expressed. Essentially anywhere in the process of gene expression from transcription, RNA processing, translation, and post-translational modifications of the protein is subject to regulation. As transcription is the first step in the process of gene expression, it is the first level of regulation for influencing the cell phenotype. The actions of transcription factors, histone modifiers, and other proteins work together to influence RNA polymerase's ability to complete the process of transcription. The actions of transcription factors are able to influence transcription by controlling the ability of RNA polymerase to be recruited to the start of a protein coding region and histone modifiers can rearrange the histones of the chromatin causing entire regions of a chromosome to become exposed or sequestered. These transcriptional regulators are able to work in a combinatorial fashion with one another to either activate and/or repress wide repertoires of transcriptional targets. Mapping out a network of interactions between these transcriptional regulators in gene expression programs allows researchers to understand how each protein is able to influence the phenotype of the cell, and how mutations to any of these transcriptional regulators are able to drive the cell into a diseased state. In the case of cancer, changes in the mechanisms of gene regulation brought on by mutations to these transcriptional regulators may drive the cell's hyper proliferative state. With the creation of next generation sequencing researchers are now better able to define where regulation is taking place in the genome, and how much it is able to influence gene expression. This gives researchers the ability to build these gene regulatory networks and evaluate their impact on gene expression. The subsequent chapters of this dissertation are a reflection of my published work investigating the contribution of oncogenic processes to gene regulatory networks in cancer through the study of hyperactivating somatic mutation of a histone modifier, changes in transcription factor response element specificity, epigenetic regulation of transcription factor signaling, and a transcription factor coactivation network.

Chromatin and Gene Regulation

Chromatin and Gene Regulation PDF Author: Bryan M. Turner
Publisher: John Wiley & Sons
ISBN: 0470751673
Category : Science
Languages : en
Pages : 288

View

Book Description
Written in an informal and accessible style, Chromatin and Gene Regulation enables the reader to understand the science of this rapidly moving field. Chromatin is a fundamental component in the network of controls that regulates gene expression. Many human diseases have been linked to disruption of these control processes by genetic or environmental factors, and unravelling the mechanisms by which they operate is one of the most exciting and rapidly developing areas of modern biology. Chromatin is central both to the rapid changes in gene transcription by which cells respond to changes in their environment and also to the maintenance of gene expression patterns from one cell generation to the next. This book will be an invaluable guide to undergraduate and postgraduate students in the biological sciences and all those with an interest in the medical implications of aberrant gene expression.

Epigenetic Gene Regulation in Stem Cell Differentiation and Reprogramming

Epigenetic Gene Regulation in Stem Cell Differentiation and Reprogramming PDF Author: Kevin Huang
Publisher:
ISBN:
Category :
Languages : en
Pages : 223

View

Book Description
The regulatory capacities of epigenetic mechanisms including DNA methylation, histone modifications, and non-coding RNAs, have seen a rising interest in recent years. These epigenetic marks are pervasive and non-randomly distributed across the genome, raising intriguing questions on how epigenetics contributes to genomic features that define cellular identity and function. Unlike fixed genetic information that is shared between all cell types, epigenetics involve multiple layers of regulation and can vary dramatically across different cell types and genomic contexts. Thus, much more effort is required to procure a complete perspective of the manifold epigenetic landscape. The body of work in this dissertation focuses on epigenetic studies in the mammalian pluripotent stem cell model system. We utilize high-throughput technologies such as microarrays and next-generation sequencing (NGS) as well as leverage existing epigenetic maps to address a wide range of molecular questions on a comprehensive global scale. This dissertation is organized into three overarching themes: First, we employed genome-wide gene expression and DNA methylation profiling tools to determine whether different cell types display unique biomarkers that can be used to distinguish them from other cell types (Chapters 2-5). We found that human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) carry distinct features in both gene expression and DNA methylation patterns, arguing in favor of the idea that these two pluripotent cell types are different. Furthermore, we compared pluripotent stem cell derived retinal pigmented epithelium (hESC-RPE and hiPSC-RPE) with fetal and adult RPE and found that all RPE cells share a core set of signature genes that distinguishes them from all other cell types. We propose these signature genes will be useful for evaluating the quality of stem-cell derived RPE. Finally, novel corneal endothelial cells (CECs) biomarkers were identified through comparing 12 other tissue types, paving the way for future studies to evaluate properties of stem-cell derived CECs. We next examined how molecular features of pluripotent stem cells are altered during the differentiation process of stem cells (Chapters 6-8). Using the RPE differentiation paradigm, we profiled both microRNA and DNA methylation patterns in intermediate stages between pluripotent stem cells and mature RPE. These two separate studies identified subsets of dynamically regulated epigenetic marks, some of which are associated with RPE signature gene expression. Furthermore, we used a highly innovative and powerful single-cell RNA-sequencing approach to profile transcriptional changes in the early embryo beginning from mature oocyte to morula stages. This study identified a conserved genetic program describing a highly dynamic transcriptional architecture during early embryogenesis. Finally, we took a focused analysis on how DNA methyltransferases contribute to shaping the pluripotent stem cell epigenome (Chapters 9-10). Using mouse ESCs null of DNA methylation, we determined DNA methylation regulates a large set of genes through action with H3K27me3. Furthermore, we determined shared and unique genomic targets of each DNA methyltransferase, including novel de novo methylation activity for Dnmt1 in vivo. In the human model system, we generated iPSCs from ICF Syndrome patient fibroblasts which carry double heterozygous mutations in DNMT3B. We found DNMT3B is involved in a wave of de novo methylation during the reprogramming process and has unique genomic targets.

Epigenetic Gene Regulation in Mouse Embryonic Stem Cells and the Developing Central Nervous System

Epigenetic Gene Regulation in Mouse Embryonic Stem Cells and the Developing Central Nervous System PDF Author: Shaun David Fouse
Publisher:
ISBN:
Category :
Languages : en
Pages : 316

View

Book Description


Non-coding RNAs and Epigenetic Regulation of Gene Expression

Non-coding RNAs and Epigenetic Regulation of Gene Expression PDF Author: Kevin V. Morris
Publisher: Horizon Scientific Press
ISBN: 9781904455943
Category : Science
Languages : en
Pages : 216

View

Book Description
Non-coding RNAs potentially play an active role in modulating gene transcription and epigenetic states. Several genes in differentiated cells may be under some form of RNA-based transcriptional and epigenetic regulatory control. This form of regulation may be controlled by selective pressures and influence the adaptability of the cell. The concept that RNA can control epigenetic states impacts our understanding of the basic fabric of the cell and may have therapeutic potential. Many studies have been carried out on the modulation of gene transcription by non-coding RNAs. This book, written by a group of distinguished scientists, represents an important overview and summary of the field to date. The 13 chapters are organized into three sections: a) Non-coding RNAs: Form, Function and Diversity; b) Non-coding RNAs: Gene Regulation and Epigenetics; and c) Non-coding RNAs: Disease and Therapeutics. This up-to-date volume is an essential book for those working in the area and represents a major information resource on current research in the fast-moving fields of epigenetics, the regulation of gene expression, and RNA research.

Recent Advances of Epigenetics in Crop Biotechnology

Recent Advances of Epigenetics in Crop Biotechnology PDF Author: Clelia De-la-Peña
Publisher: Frontiers Media SA
ISBN: 2889198545
Category :
Languages : en
Pages :

View

Book Description
Epigenetics is a new field that explains gene expression at the chromatin structure and organization level. Three principal epigenetic mechanisms are known and hundreds of combinations among them can develop different phenotypic characteristics. DNA methylation, histone modifications and small RNAs have been identified, and their functions are being studied in order to understand the mechanisms of interaction and regulation among the different biological processes in plants. Although, fundamental epigenetic mechanisms in crop plants are beginning to be elucidated, the comprehension of the different epigenetic mechanisms, by which plant gene regulation and phenotype are modified, is a major topic to develop in the near future in order to increase crop productivity. Thus, the importance of epigenetics in improving crop productivity is undoubtedly growing. Current research on epigenetics suggest that DNA methylation, histone modifications and small RNAs are involved in almost every aspect of plant life including agronomically important traits such as flowering time, fruit development, responses to environmental factors, defense response and plant growth. The aim of this Research Topic is to explore the recent advances concerning the role of epigenetics in crop biotechnology, as well as to enhance and promote interactions among high quality researchers from different disciplines such as genetics, cell biology, pathology, microbiology, and evolutionary biology in order to join forces and decipher the epigenetic mechanisms in crop productivity.

Regulation of gene expression

Regulation of gene expression PDF Author: U Satyanarayana
Publisher: Elsevier Health Sciences
ISBN: 8131241831
Category : Medical
Languages : en
Pages : 21

View

Book Description
Regulation of gene expression Regulation of gene expression

Long-Range Control of Gene Expression

Long-Range Control of Gene Expression PDF Author: Veronica van Heyningen
Publisher: Academic Press
ISBN: 9780080877815
Category : Science
Languages : en
Pages : 416

View

Book Description
Long-Range Control of Gene Expression covers the current progress in understanding the mechanisms for genomic control of gene expression, which has grown considerably in the last few years as insight into genome organization and chromatin regulation has advanced. Discusses the evolution of cis-regulatory sequences in drosophila Includes information on genomic imprinting and imprinting defects in humans Includes a chapter on epigenetic gene regulation in cancer