Deciphering the Gene Expression Control in Epigenetic, Post-transcriptional and Translational Regulation

Deciphering the Gene Expression Control in Epigenetic, Post-transcriptional and Translational Regulation PDF Author: Jianan Lin
Publisher:
ISBN:
Category : Electronic dissertations
Languages : en
Pages :

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Book Description
Regulation of gene expression, through which cells increase or decrease the gene products, is an essential part of development, which not only determines the cellular differentiation but also responds to the environmental changes. A wide range of gene regulation mechanisms are involved in two major processes, from Deoxyribonucleic acid (DNA) to Ribonucleic acid (RNA), and from RNA to protein, also known as transcription and translation, respectively. Though the regulation of gene expression is not fully understood, this complex process has been characterized to several major steps, which includes epigenetic regulation, transcriptional regulation, post-transcriptional regulation and translational regulation. The present study covers three main projects related to three of the aforementioned steps of gene regulation. First, we study the DNA methylation dynamics in the bovine early embryos. To understand the epigenetic reprogramming and regulation in the embryonic development, we characterize the methylation process at the single-base level in early embryos. Second, we develop a novel method, called Protein-RNA Association Strength (PRAS), to predict the functional targets of RNA-Binding Proteins (RBPs) that play important roles in the regulation of gene expression in the post-transcriptional process. The development of various Cross-linking and immunoprecipitation with high-throughput sequencing (CLIP-seq) data makes it possible to investigate the transcriptomic binding sites of RBPs. We aim to fill the gap between the peak-calling methods and the interpretation of RBPs' biological functions based on CLIP-seq data. Third, we study the regulation of c-MYC on the mRNA translation. The oncogenic c-MYC (MYC) transcription factor has broad effects on gene expression and cell behavior. We study how MYC affects the global translation of mRNAs and the translation start-site usage in the human lymphoma cell line. In sum, we perform data analysis and methodology development in these three specific projects related to the regulation of gene expression, which will help us better understand the central dogma of biology.

Post-transcriptional Gene Regulation in Human Disease

Post-transcriptional Gene Regulation in Human Disease PDF Author: Buddhi Prakash Jain
Publisher: Academic Press
ISBN: 0323914241
Category : Medical
Languages : en
Pages : 396

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Book Description
Post-transcriptional Gene Regulation in Human Disease, a new volume in the Translational Epigenetics book series, offers a thorough overview and discussion of post-transcriptional genetic control mechanisms and their roles across various pathologies and human developmental outcomes, along with regulatory mechanisms targeted for therapeutic approaches. The book is broadly divided in two parts: early chapters describe the basics of post-transcriptional gene regulation, associated epigenetic mechanisms, the role of RNA binding proteins, the evolution of post-transcriptional gene regulation, and methods to study these mechanisms. The second half of the book includes deeper discussion of post-transcriptional gene regulation across specific diseases and therapeutics targets. Various post-transcriptional events, including alternative splicing and polyadenylation, mRNA stability, and miRNAs and their involvement in the disease progression, are examined in detail. Includes full-color imagery illustrating key concepts and post-transcriptional disease processes, as well as descriptions of methods for studying post-transcriptional gene regulation Presents fundamental knowledge, molecular and biochemical mechanisms, and recent findings in concise and easily understandable formats Features a summary and conclusion at the end of each chapter

The Histone Code and Beyond

The Histone Code and Beyond PDF Author: Shelley L. Berger
Publisher: Springer Science & Business Media
ISBN: 354037633X
Category : Science
Languages : en
Pages : 215

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Book Description
Methylation of DNA at cytosine residues as well as post-translational modifications of histones, including phosphorylation, acetylation, methylation and ubiquitylation, contribute to the epigenetic information carried by chromatin. These changes play an important role in the regulation of gene expression by modulating the access of regulatory factors to the DNA. The use of a combination of biochemical, genetic and structural approaches has allowed demonstration of the role of chromatin structure in transcriptional control. The structure of nucleosomes has been elucidated and enzymes involved in DNA or histone modifications have been extensively characterized. Since deregulation of epigenetic marks has been reported in many cancers, a better understanding of the underlying molecular mechanisms bears the promise that new drug targets may soon be found. The newest developments in this quickly developing field are presented in this book.

The Histone Code and Beyond

The Histone Code and Beyond PDF Author: Shelley L. Berger
Publisher: Springer
ISBN: 9783540813231
Category : Science
Languages : en
Pages : 215

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Book Description
Methylation of DNA at cytosine residues as well as post-translational modifications of histones, including phosphorylation, acetylation, methylation and ubiquitylation, contribute to the epigenetic information carried by chromatin. These changes play an important role in the regulation of gene expression by modulating the access of regulatory factors to the DNA. The use of a combination of biochemical, genetic and structural approaches has allowed demonstration of the role of chromatin structure in transcriptional control. The structure of nucleosomes has been elucidated and enzymes involved in DNA or histone modifications have been extensively characterized. Since deregulation of epigenetic marks has been reported in many cancers, a better understanding of the underlying molecular mechanisms bears the promise that new drug targets may soon be found. The newest developments in this quickly developing field are presented in this book.

Biochemistry and Molecular Biology

Biochemistry and Molecular Biology PDF Author: Alison Snape
Publisher: Oxford University Press
ISBN: 0199609497
Category : Science
Languages : en
Pages : 591

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Book Description
Now in its fifth edition Biochemistry and Molecular Biology features a new author team, who have retained the much-praised clarity of previous editions, while adding a more biomedical focus and incorporating a discussion of recent developments in research. A new chapter on the general principles of nutrition emphasises the key principles underlying complex metabolic pathways, enabling students to appreciate an integrated view of human metabolism and nutrition. Also new to the fifth edition, a chapter on the control of gene expression reflects ourincreasing understanding of the importance and power of gene regulation. With an integrated approach covering both biochemistry and molecular biology, complemented by frequent diagrams and clear explanations, and all presented in a broader cellular context, this text is the perfect introduction for any student new to the subject. Online Resource Centre: The Online Resource Centre features: For registered adopters of the book: DTFigures from the book available to download For students: DT Further reading organised by chapter, linked to the book via QR codesDT An extensive bank of multiple-choice questions for self-directed learningDT Links to 3D molecular structures

ROS Regulation during Plant Abiotic Stress Responses

ROS Regulation during Plant Abiotic Stress Responses PDF Author: Zhulong Chan
Publisher: Frontiers Media SA
ISBN: 2889450546
Category :
Languages : en
Pages :

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Book Description
Plants are continuously exposed to a wide range of environmental conditions, including cold, drought, salt, heat, which have major impact on plant growth and development. To survive, plants have evolved complex physiological and biochemical adaptations to cope with a variety of adverse environmental stresses. Among them, reactive oxygen species (ROS) are key regulators and play pivotal roles during plant stress responses, which are thought to function as early signals during plant abiotic stress responses. ROS were long regarded as unwanted and toxic by-products of physiological metabolism. However, ROS are now recognized as central players in the complex signaling network of cells. Therefore, a fine-tuning control between ROS production and scavenging pathways is essential to maintain non-toxic levels in planta under stressful conditions through enzymatic and non-enzymatic antioxidant defense systems. We focus on the roles of ROS during plant abiotic stress responses in this Research Topic. Plant responses to multiple abiotic stresses and effects of hormones and chemicals on plant stress responses have been carefully studies. Although functions of several stress responsive genes have been characterized and possible interactions between hormones and ROS are discussed, future researches are needed to functionally characterize ROS regulatory and signaling transduction pathways.

Epigenetic Modifications Associated with Abiotic and Biotic Stresses in Plants: An Implication for Understanding Plant Evolution

Epigenetic Modifications Associated with Abiotic and Biotic Stresses in Plants: An Implication for Understanding Plant Evolution PDF Author: Mahmoud W. Yaish
Publisher: Frontiers Media SA
ISBN: 2889453812
Category :
Languages : en
Pages :

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Book Description
Alterations in gene expression are essential during growth and development phases and when plants are exposed to environmental challenges. Stress conditions induce gene expression modifications, which are associated with changes in the biochemical and physiological processes that help plants to avoid or reduce potential damage resulting from these stresses. After exposure to stress, surviving plants tend to flower earlier than normal and therefore transfer the accumulated epigenetic information to their progenies, given that seeds, where this information is stored, are formed at a later stage of plant development. DNA methylation is correlated with expression repression. Likewise, miRNA produced in the cell can reduce the transcript abundance or even prevent translation of mRNA. However, histone modulation, such as histone acetylation, methylation, and ubiquitination, can show distinct effects on gene expression. These alterations can be inherited, especially if the plants are consistently exposed to a particular environmental stress. Retrotransposons and retroviruses are foreign movable DNA elements that play an important role in plant evolution. Recent studies have shown that epigenetic alterations control the movement and the expression of genes harbored within these elements. These epigenetic modifications have an impact on the morphology, and biotic and abiotic tolerance in the subsequent generations because they can be inherited through the transgenerational memory in plants. Therefore, epigenetic modifications, including DNA methylation, histone modifications, and small RNA interference, serve not only to alter gene expression but also may enhance the evolutionary process in eukaryotes. In this E-book, original research and review articles that cover issues related to the role of DNA methylation, histone modifications, and small RNA in plant transgenerational epigenetic memory were published. The knowledge published on this topic may add new insight on the involvement of epigenetic factors in natural selection and environmental adaptation. This information may also help to generate a modeling system to study the epigenetic role in evolution.

Clinical Applications of Pharmacogenetics

Clinical Applications of Pharmacogenetics PDF Author: Despina Sanoudou
Publisher: BoD – Books on Demand
ISBN: 953510389X
Category : Medical
Languages : en
Pages : 306

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Book Description
The rapidly evolving field of Pharmacogenetics aims at identifying the genetic factors implicated in the inter-individual variation of drug response. These factors could enable patient sub-classification based on their treatment needs thus expediting drug development and promoting personalized, safer and more effective treatments. This book presents Pharmacogenetic examples from a broad spectrum of different drugs, for different diseases, which are representative of different stages of evaluation or application. It has been designed so as to serve both the unfamiliar reader through explanations of basic Pharmacogenetic concepts, the clinician with presentation of the latest developments and international guidelines, and the research scientist with examples of Pharmacogenetic applications, discussions on the limitations and an outlook on the new scientific trends in this field.

Deciphering the Gene Expression Control in Epigenetic, Post-transcriptional and Translational Regulation

Deciphering the Gene Expression Control in Epigenetic, Post-transcriptional and Translational Regulation PDF Author: Jianan Lin
Publisher:
ISBN:
Category : Electronic dissertations
Languages : en
Pages :

View

Book Description
Regulation of gene expression, through which cells increase or decrease the gene products, is an essential part of development, which not only determines the cellular differentiation but also responds to the environmental changes. A wide range of gene regulation mechanisms are involved in two major processes, from Deoxyribonucleic acid (DNA) to Ribonucleic acid (RNA), and from RNA to protein, also known as transcription and translation, respectively. Though the regulation of gene expression is not fully understood, this complex process has been characterized to several major steps, which includes epigenetic regulation, transcriptional regulation, post-transcriptional regulation and translational regulation. The present study covers three main projects related to three of the aforementioned steps of gene regulation. First, we study the DNA methylation dynamics in the bovine early embryos. To understand the epigenetic reprogramming and regulation in the embryonic development, we characterize the methylation process at the single-base level in early embryos. Second, we develop a novel method, called Protein-RNA Association Strength (PRAS), to predict the functional targets of RNA-Binding Proteins (RBPs) that play important roles in the regulation of gene expression in the post-transcriptional process. The development of various Cross-linking and immunoprecipitation with high-throughput sequencing (CLIP-seq) data makes it possible to investigate the transcriptomic binding sites of RBPs. We aim to fill the gap between the peak-calling methods and the interpretation of RBPs' biological functions based on CLIP-seq data. Third, we study the regulation of c-MYC on the mRNA translation. The oncogenic c-MYC (MYC) transcription factor has broad effects on gene expression and cell behavior. We study how MYC affects the global translation of mRNAs and the translation start-site usage in the human lymphoma cell line. In sum, we perform data analysis and methodology development in these three specific projects related to the regulation of gene expression, which will help us better understand the central dogma of biology.

Post-transcriptional Gene Regulation in Human Disease

Post-transcriptional Gene Regulation in Human Disease PDF Author: Buddhi Prakash Jain
Publisher: Academic Press
ISBN: 0323914241
Category : Medical
Languages : en
Pages : 396

View

Book Description
Post-transcriptional Gene Regulation in Human Disease, a new volume in the Translational Epigenetics book series, offers a thorough overview and discussion of post-transcriptional genetic control mechanisms and their roles across various pathologies and human developmental outcomes, along with regulatory mechanisms targeted for therapeutic approaches. The book is broadly divided in two parts: early chapters describe the basics of post-transcriptional gene regulation, associated epigenetic mechanisms, the role of RNA binding proteins, the evolution of post-transcriptional gene regulation, and methods to study these mechanisms. The second half of the book includes deeper discussion of post-transcriptional gene regulation across specific diseases and therapeutics targets. Various post-transcriptional events, including alternative splicing and polyadenylation, mRNA stability, and miRNAs and their involvement in the disease progression, are examined in detail. Includes full-color imagery illustrating key concepts and post-transcriptional disease processes, as well as descriptions of methods for studying post-transcriptional gene regulation Presents fundamental knowledge, molecular and biochemical mechanisms, and recent findings in concise and easily understandable formats Features a summary and conclusion at the end of each chapter

The Histone Code and Beyond

The Histone Code and Beyond PDF Author: Shelley L. Berger
Publisher: Springer Science & Business Media
ISBN: 354037633X
Category : Science
Languages : en
Pages : 215

View

Book Description
Methylation of DNA at cytosine residues as well as post-translational modifications of histones, including phosphorylation, acetylation, methylation and ubiquitylation, contribute to the epigenetic information carried by chromatin. These changes play an important role in the regulation of gene expression by modulating the access of regulatory factors to the DNA. The use of a combination of biochemical, genetic and structural approaches has allowed demonstration of the role of chromatin structure in transcriptional control. The structure of nucleosomes has been elucidated and enzymes involved in DNA or histone modifications have been extensively characterized. Since deregulation of epigenetic marks has been reported in many cancers, a better understanding of the underlying molecular mechanisms bears the promise that new drug targets may soon be found. The newest developments in this quickly developing field are presented in this book.

Functionele Genoom in Kiemceltumoren

Functionele Genoom in Kiemceltumoren PDF Author:
Publisher:
ISBN: 9789053359334
Category :
Languages : en
Pages : 253

View

Book Description


RNA Modifications and Epitranscriptomics

RNA Modifications and Epitranscriptomics PDF Author: Xiao Han
Publisher: Frontiers Media SA
ISBN: 2889761061
Category : Science
Languages : en
Pages :

View

Book Description


The Histone Code and Beyond

The Histone Code and Beyond PDF Author: Shelley L. Berger
Publisher: Springer
ISBN: 9783540813231
Category : Science
Languages : en
Pages : 215

View

Book Description
Methylation of DNA at cytosine residues as well as post-translational modifications of histones, including phosphorylation, acetylation, methylation and ubiquitylation, contribute to the epigenetic information carried by chromatin. These changes play an important role in the regulation of gene expression by modulating the access of regulatory factors to the DNA. The use of a combination of biochemical, genetic and structural approaches has allowed demonstration of the role of chromatin structure in transcriptional control. The structure of nucleosomes has been elucidated and enzymes involved in DNA or histone modifications have been extensively characterized. Since deregulation of epigenetic marks has been reported in many cancers, a better understanding of the underlying molecular mechanisms bears the promise that new drug targets may soon be found. The newest developments in this quickly developing field are presented in this book.

Biochemistry and Molecular Biology

Biochemistry and Molecular Biology PDF Author: Alison Snape
Publisher: Oxford University Press
ISBN: 0199609497
Category : Science
Languages : en
Pages : 591

View

Book Description
Now in its fifth edition Biochemistry and Molecular Biology features a new author team, who have retained the much-praised clarity of previous editions, while adding a more biomedical focus and incorporating a discussion of recent developments in research. A new chapter on the general principles of nutrition emphasises the key principles underlying complex metabolic pathways, enabling students to appreciate an integrated view of human metabolism and nutrition. Also new to the fifth edition, a chapter on the control of gene expression reflects ourincreasing understanding of the importance and power of gene regulation. With an integrated approach covering both biochemistry and molecular biology, complemented by frequent diagrams and clear explanations, and all presented in a broader cellular context, this text is the perfect introduction for any student new to the subject. Online Resource Centre: The Online Resource Centre features: For registered adopters of the book: DTFigures from the book available to download For students: DT Further reading organised by chapter, linked to the book via QR codesDT An extensive bank of multiple-choice questions for self-directed learningDT Links to 3D molecular structures

ROS Regulation during Plant Abiotic Stress Responses

ROS Regulation during Plant Abiotic Stress Responses PDF Author: Zhulong Chan
Publisher: Frontiers Media SA
ISBN: 2889450546
Category :
Languages : en
Pages :

View

Book Description
Plants are continuously exposed to a wide range of environmental conditions, including cold, drought, salt, heat, which have major impact on plant growth and development. To survive, plants have evolved complex physiological and biochemical adaptations to cope with a variety of adverse environmental stresses. Among them, reactive oxygen species (ROS) are key regulators and play pivotal roles during plant stress responses, which are thought to function as early signals during plant abiotic stress responses. ROS were long regarded as unwanted and toxic by-products of physiological metabolism. However, ROS are now recognized as central players in the complex signaling network of cells. Therefore, a fine-tuning control between ROS production and scavenging pathways is essential to maintain non-toxic levels in planta under stressful conditions through enzymatic and non-enzymatic antioxidant defense systems. We focus on the roles of ROS during plant abiotic stress responses in this Research Topic. Plant responses to multiple abiotic stresses and effects of hormones and chemicals on plant stress responses have been carefully studies. Although functions of several stress responsive genes have been characterized and possible interactions between hormones and ROS are discussed, future researches are needed to functionally characterize ROS regulatory and signaling transduction pathways.

Epigenetic Modifications Associated with Abiotic and Biotic Stresses in Plants: An Implication for Understanding Plant Evolution

Epigenetic Modifications Associated with Abiotic and Biotic Stresses in Plants: An Implication for Understanding Plant Evolution PDF Author: Mahmoud W. Yaish
Publisher: Frontiers Media SA
ISBN: 2889453812
Category :
Languages : en
Pages :

View

Book Description
Alterations in gene expression are essential during growth and development phases and when plants are exposed to environmental challenges. Stress conditions induce gene expression modifications, which are associated with changes in the biochemical and physiological processes that help plants to avoid or reduce potential damage resulting from these stresses. After exposure to stress, surviving plants tend to flower earlier than normal and therefore transfer the accumulated epigenetic information to their progenies, given that seeds, where this information is stored, are formed at a later stage of plant development. DNA methylation is correlated with expression repression. Likewise, miRNA produced in the cell can reduce the transcript abundance or even prevent translation of mRNA. However, histone modulation, such as histone acetylation, methylation, and ubiquitination, can show distinct effects on gene expression. These alterations can be inherited, especially if the plants are consistently exposed to a particular environmental stress. Retrotransposons and retroviruses are foreign movable DNA elements that play an important role in plant evolution. Recent studies have shown that epigenetic alterations control the movement and the expression of genes harbored within these elements. These epigenetic modifications have an impact on the morphology, and biotic and abiotic tolerance in the subsequent generations because they can be inherited through the transgenerational memory in plants. Therefore, epigenetic modifications, including DNA methylation, histone modifications, and small RNA interference, serve not only to alter gene expression but also may enhance the evolutionary process in eukaryotes. In this E-book, original research and review articles that cover issues related to the role of DNA methylation, histone modifications, and small RNA in plant transgenerational epigenetic memory were published. The knowledge published on this topic may add new insight on the involvement of epigenetic factors in natural selection and environmental adaptation. This information may also help to generate a modeling system to study the epigenetic role in evolution.

Clinical Applications of Pharmacogenetics

Clinical Applications of Pharmacogenetics PDF Author: Despina Sanoudou
Publisher: BoD – Books on Demand
ISBN: 953510389X
Category : Medical
Languages : en
Pages : 306

View

Book Description
The rapidly evolving field of Pharmacogenetics aims at identifying the genetic factors implicated in the inter-individual variation of drug response. These factors could enable patient sub-classification based on their treatment needs thus expediting drug development and promoting personalized, safer and more effective treatments. This book presents Pharmacogenetic examples from a broad spectrum of different drugs, for different diseases, which are representative of different stages of evaluation or application. It has been designed so as to serve both the unfamiliar reader through explanations of basic Pharmacogenetic concepts, the clinician with presentation of the latest developments and international guidelines, and the research scientist with examples of Pharmacogenetic applications, discussions on the limitations and an outlook on the new scientific trends in this field.