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

Get Book

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.

Theoretical and Applied Aspects of Systems Biology

Theoretical and Applied Aspects of Systems Biology PDF Author: Fabricio Alves Barbosa da Silva
Publisher: Springer
ISBN: 3319749749
Category : Computers
Languages : en
Pages : 259

Get Book

Book Description
This book presents the theoretical foundations of Systems Biology, as well as its application in studies on human hosts, pathogens and associated diseases. This book presents several chapters written by renowned experts in the field. Some topics discussed in depth in this book include: computational modeling of multiresistant bacteria, systems biology of cancer, systems immunology, networks in systems biology.

A Systems Biology Approach to Advancing Adverse Outcome Pathways for Risk Assessment

A Systems Biology Approach to Advancing Adverse Outcome Pathways for Risk Assessment PDF Author: Natàlia Garcia-Reyero
Publisher: Springer
ISBN: 3319660845
Category : Science
Languages : en
Pages : 422

Get Book

Book Description
Social pressure to minimize the use of animal testing, the ever-increasing concern on animal welfare, and the need for more human-relevant and more predictive toxicity tests are some of the drivers for new approaches to chemical screening. This book focuses on The Adverse Outcome Pathway, an analytical construct that describes a sequential chain of causally linked events at different levels of biological organization that lead to an adverse health or ecotoxicological effect. While past efforts have focused on toxicological pathway-based vision for human and ecological health assessment relying on in vitro systems and predictive models, The Adverse Outcome Pathway framework provides a simplified and structured way to organize toxicological information. Within the book, a systems biology approach supplies the tools to infer, link, and quantify the molecular initiating events and the key events and key event relationships leading to adverse outcomes. The advancement of these tools is crucial for the successful implementation of AOPs for regulatory purposes.

Aging and Health - A Systems Biology Perspective

Aging and Health - A Systems Biology Perspective PDF Author: A.I. Yashin
Publisher: Karger Medical and Scientific Publishers
ISBN: 3318027308
Category : Science
Languages : en
Pages : 206

Get Book

Book Description
Aging is a major risk factor for chronic diseases, which in turn can provide information about the aging of a biological system. This publication serves as an introduction to systems biology and its application to biological aging. Key pathways and processes that impinge on aging are reviewed, and how they contribute to health and disease during aging is discussed. The evolution of this situation is analyzed, and the consequences for the study of genetic effects on aging are presented. Epigenetic programming of aging, as a continuation of development, creates an interface between the genome and the environment. New research into the gut microbiome describes how this interface may operate in practice with marked consequences for a variety of disorders. This analysis is bolstered by a view of the aging organism as a whole, with conclusions about the mechanisms underlying resilience of the organism to change, and is expanded with a discussion of circadian rhythms in aging. Finally, the book presents an outlook for the development of interventions to delay or to reverse the features of aging. The publication is recommended to students, researchers as well as professionals dealing with public health and public policy related to an aging society.

The Analysis of Regulatory DNA: Current Developments, Knowledge and Applications Uncovering Gene Regulation

The Analysis of Regulatory DNA: Current Developments, Knowledge and Applications Uncovering Gene Regulation PDF Author: Kenneth Berendzen
Publisher: Bentham Science Publishers
ISBN: 1608054926
Category : Science
Languages : en
Pages : 225

Get Book

Book Description
A major goal of integrative research is understanding regulatory networks to such an extent as to allow researchers to model developmental and stress responses. Regulatory networks of living systems include complex and vast interactions between proteins, metabolites, RNA, various signaling molecules and DNA. One aspect of systems biology is understanding the dynamics of protein-DNA interactions affecting gene expression that are caused by transcription factors (TFs) and chromatin remodeling factors. This e-book provides a resource for summarizing current knowledge eukaryotic transcription and explores cis-elements and methods for their analysis, prediction and discovery. The book also presents an overview of exploring gene regulatory networks, chromatin, and miRNAs. Information about state-of-the-art techniques for the determination of TF - cis-element interactions in vivo and in silico give cutting edge insights on how genomic-scale research is being approached. The Analysis of Regulatory DNA provides readers with both the necessary background knowledge and provocative, up-to-date insights aimed at sparking new and vibrant experimental designs for understanding and predicting cis-elements in the eukaryotic genome.

Epigenetics and Systems Biology

Epigenetics and Systems Biology PDF Author: Leonie Ringrose
Publisher: Academic Press
ISBN: 0128030763
Category : Medical
Languages : en
Pages : 286

Get Book

Book Description
Epigenetics and Systems Biology highlights the need for collaboration between experiments and theoretical modeling that is required for successful application of systems biology in epigenetics studies. This book breaks down the obstacles which exist between systems biology and epigenetics researchers due to information barriers and segmented research, giving real-life examples of successful combinations of systems biology and epigenetics experiments. Each section covers one type of modeling and one set of epigenetic questions on which said models have been successfully applied. In addition, the book highlights how modeling and systems biology relate to studies of RNA, DNA, and genome instability, mechanisms of DNA damage signaling and repair, and the effect of the environment on genome stability. Presents original research in a wider perspective to reveal potential for synergies between the two fields of study Provides the latest experiments in primary literature for the modeling audience Includes chapters written by experts in systems biology and epigenetics who have vast experience studying clinical applications

Weighted Network Analysis

Weighted Network Analysis PDF Author: Steve Horvath
Publisher: Springer Science & Business Media
ISBN: 144198819X
Category : Science
Languages : en
Pages : 421

Get Book

Book Description
High-throughput measurements of gene expression and genetic marker data facilitate systems biologic and systems genetic data analysis strategies. Gene co-expression networks have been used to study a variety of biological systems, bridging the gap from individual genes to biologically or clinically important emergent phenotypes.

Towards a Theory of Development

Towards a Theory of Development PDF Author: Alessandro Minelli
Publisher: Oxford University Press
ISBN: 0199671427
Category : Science
Languages : en
Pages : 283

Get Book

Book Description
Is it possible to explain and predict the development of living things? What is development? Answers to these innocuous questions are far from straightforward. To date, no systematic, targeted effort has been made to construct a unifying theory of development. This text offers a unique exploration of the foundations of ontogeny by asking how the development of living things should be understood. It explores the key concepts of developmental biology, asks whether general principles of development can be discovered, and examines the role of models and theories. This book analyses a wealth of approaches to concepts, models and theories of development, such as gene regulatory networks, accounts based on systems biology and on physics of soft matter, the different articulations of evolution and development, symbiont-induced development, as well as the widely discussed concepts of positional information and morphogenetic field, the idea of a 'programme' of development and its critiques, and the long-standing opposition between preformationist and epigenetic conceptions of development. --

Transactions on Computational Systems Biology XI

Transactions on Computational Systems Biology XI PDF Author: Corrado Priami
Publisher: Springer Science & Business Media
ISBN: 364204185X
Category : Computers
Languages : en
Pages : 335

Get Book

Book Description
This issue on Computational Models for Cell Processes is based on a workshop that took place in Turku, Finland, May 2008. The papers span a mix of approaches to systems biology, ranging from quantitative techniques to computing paradigms inspired by biology.

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.

Theoretical and Applied Aspects of Systems Biology

Theoretical and Applied Aspects of Systems Biology PDF Author: Fabricio Alves Barbosa da Silva
Publisher: Springer
ISBN: 3319749749
Category : Computers
Languages : en
Pages : 259

View

Book Description
This book presents the theoretical foundations of Systems Biology, as well as its application in studies on human hosts, pathogens and associated diseases. This book presents several chapters written by renowned experts in the field. Some topics discussed in depth in this book include: computational modeling of multiresistant bacteria, systems biology of cancer, systems immunology, networks in systems biology.

A Systems Biology Approach to Advancing Adverse Outcome Pathways for Risk Assessment

A Systems Biology Approach to Advancing Adverse Outcome Pathways for Risk Assessment PDF Author: Natàlia Garcia-Reyero
Publisher: Springer
ISBN: 3319660845
Category : Science
Languages : en
Pages : 422

View

Book Description
Social pressure to minimize the use of animal testing, the ever-increasing concern on animal welfare, and the need for more human-relevant and more predictive toxicity tests are some of the drivers for new approaches to chemical screening. This book focuses on The Adverse Outcome Pathway, an analytical construct that describes a sequential chain of causally linked events at different levels of biological organization that lead to an adverse health or ecotoxicological effect. While past efforts have focused on toxicological pathway-based vision for human and ecological health assessment relying on in vitro systems and predictive models, The Adverse Outcome Pathway framework provides a simplified and structured way to organize toxicological information. Within the book, a systems biology approach supplies the tools to infer, link, and quantify the molecular initiating events and the key events and key event relationships leading to adverse outcomes. The advancement of these tools is crucial for the successful implementation of AOPs for regulatory purposes.

Aging and Health - A Systems Biology Perspective

Aging and Health - A Systems Biology Perspective PDF Author: A.I. Yashin
Publisher: Karger Medical and Scientific Publishers
ISBN: 3318027308
Category : Science
Languages : en
Pages : 206

View

Book Description
Aging is a major risk factor for chronic diseases, which in turn can provide information about the aging of a biological system. This publication serves as an introduction to systems biology and its application to biological aging. Key pathways and processes that impinge on aging are reviewed, and how they contribute to health and disease during aging is discussed. The evolution of this situation is analyzed, and the consequences for the study of genetic effects on aging are presented. Epigenetic programming of aging, as a continuation of development, creates an interface between the genome and the environment. New research into the gut microbiome describes how this interface may operate in practice with marked consequences for a variety of disorders. This analysis is bolstered by a view of the aging organism as a whole, with conclusions about the mechanisms underlying resilience of the organism to change, and is expanded with a discussion of circadian rhythms in aging. Finally, the book presents an outlook for the development of interventions to delay or to reverse the features of aging. The publication is recommended to students, researchers as well as professionals dealing with public health and public policy related to an aging society.

The Analysis of Regulatory DNA: Current Developments, Knowledge and Applications Uncovering Gene Regulation

The Analysis of Regulatory DNA: Current Developments, Knowledge and Applications Uncovering Gene Regulation PDF Author: Kenneth Berendzen
Publisher: Bentham Science Publishers
ISBN: 1608054926
Category : Science
Languages : en
Pages : 225

View

Book Description
A major goal of integrative research is understanding regulatory networks to such an extent as to allow researchers to model developmental and stress responses. Regulatory networks of living systems include complex and vast interactions between proteins, metabolites, RNA, various signaling molecules and DNA. One aspect of systems biology is understanding the dynamics of protein-DNA interactions affecting gene expression that are caused by transcription factors (TFs) and chromatin remodeling factors. This e-book provides a resource for summarizing current knowledge eukaryotic transcription and explores cis-elements and methods for their analysis, prediction and discovery. The book also presents an overview of exploring gene regulatory networks, chromatin, and miRNAs. Information about state-of-the-art techniques for the determination of TF - cis-element interactions in vivo and in silico give cutting edge insights on how genomic-scale research is being approached. The Analysis of Regulatory DNA provides readers with both the necessary background knowledge and provocative, up-to-date insights aimed at sparking new and vibrant experimental designs for understanding and predicting cis-elements in the eukaryotic genome.

Epigenetics and Systems Biology

Epigenetics and Systems Biology PDF Author: Leonie Ringrose
Publisher: Academic Press
ISBN: 0128030763
Category : Medical
Languages : en
Pages : 286

View

Book Description
Epigenetics and Systems Biology highlights the need for collaboration between experiments and theoretical modeling that is required for successful application of systems biology in epigenetics studies. This book breaks down the obstacles which exist between systems biology and epigenetics researchers due to information barriers and segmented research, giving real-life examples of successful combinations of systems biology and epigenetics experiments. Each section covers one type of modeling and one set of epigenetic questions on which said models have been successfully applied. In addition, the book highlights how modeling and systems biology relate to studies of RNA, DNA, and genome instability, mechanisms of DNA damage signaling and repair, and the effect of the environment on genome stability. Presents original research in a wider perspective to reveal potential for synergies between the two fields of study Provides the latest experiments in primary literature for the modeling audience Includes chapters written by experts in systems biology and epigenetics who have vast experience studying clinical applications

Weighted Network Analysis

Weighted Network Analysis PDF Author: Steve Horvath
Publisher: Springer Science & Business Media
ISBN: 144198819X
Category : Science
Languages : en
Pages : 421

View

Book Description
High-throughput measurements of gene expression and genetic marker data facilitate systems biologic and systems genetic data analysis strategies. Gene co-expression networks have been used to study a variety of biological systems, bridging the gap from individual genes to biologically or clinically important emergent phenotypes.

Systems Biology

Systems Biology PDF Author:
Publisher:
ISBN: 981446290X
Category :
Languages : en
Pages :

View

Book Description


Towards a Theory of Development

Towards a Theory of Development PDF Author: Alessandro Minelli
Publisher: Oxford University Press
ISBN: 0199671427
Category : Science
Languages : en
Pages : 283

View

Book Description
Is it possible to explain and predict the development of living things? What is development? Answers to these innocuous questions are far from straightforward. To date, no systematic, targeted effort has been made to construct a unifying theory of development. This text offers a unique exploration of the foundations of ontogeny by asking how the development of living things should be understood. It explores the key concepts of developmental biology, asks whether general principles of development can be discovered, and examines the role of models and theories. This book analyses a wealth of approaches to concepts, models and theories of development, such as gene regulatory networks, accounts based on systems biology and on physics of soft matter, the different articulations of evolution and development, symbiont-induced development, as well as the widely discussed concepts of positional information and morphogenetic field, the idea of a 'programme' of development and its critiques, and the long-standing opposition between preformationist and epigenetic conceptions of development. --

Transactions on Computational Systems Biology XI

Transactions on Computational Systems Biology XI PDF Author: Corrado Priami
Publisher: Springer Science & Business Media
ISBN: 364204185X
Category : Computers
Languages : en
Pages : 335

View

Book Description
This issue on Computational Models for Cell Processes is based on a workshop that took place in Turku, Finland, May 2008. The papers span a mix of approaches to systems biology, ranging from quantitative techniques to computing paradigms inspired by biology.