Download or read book Chromatin Structure Mediated Regulation of Nuclear Processes written by Min Kim and published by . This book was released on 2013 with total page 99 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chromatin is a mixture of DNA and DNA binding proteins that control transcription. Dynamic chromatin structure modulates gene expression and is responsible for an extraordinary spectrum of developmental processes. An intricate interplay of DNA methylation, histone modifications, histone variants, small RNA accumulation, and ATPase chromatin remodelers defines chromatin re-configuration in a precise manner, locally within a cell and globally across different cell types. The development of high-throughput screening methods such as microarray and whole-genome sequencing has led to an explosion of chromatin studies in the past decade. Moreover, genetic and molecular studies resulted in identification of a number of proteins that may influence chromatin structure. However, the exact functions of individual proteins as well as their functional relationships to each other are less understood. Also, the role of chromatin components in establishing cell- and tissue-specific chromatin structure is largely unknown. To address these open questions in chromatin biology, I focused my dissertation work on 1) studying tissue-specific DNA demethylation in seed, and 2) determining the role of a ubiquitous DNA binding protein, linker histone H1, in regulating chromatin structure. Tissue specific DNA methylation in seed. In endosperm, the nutritive tissue that nourishes the embryo, parent-of-origin specific gene expression is regulated by DNA demethylation. However, the extent to which DNA demethylation occurs in a tissue-specific manner and regulates transcription in the endosperm of crop plants like rice remains unknown. To address these questions, my colleagues and I examined the DNA methylation patterns of two rice seed tissues, embryo and endosperm. We found that endosperm genome is globally hypomethylated at non-CG sites and locally hypomethylated at CG-sites compared to embryo. We also identified that small transposons near genes (euchromatic regions) are the primary targets of DNA demethylation. The loci near the genes preferentially expressed in endosperm (e.g. storage protein and starch synthesizing enzymes) are subjected to local hypomethylation, suggesting that DNA methylation plays a role in inducing tissue-specific genes in endosperm. The role of H1 in regulating chromatin structure. H1 is proposed to facilitate higher order chromatin structure, but its effects on individual chromatin components and transcription are less understood. To resolve this issue, we investigated the role of H1 in regulating DNA methylation, nucleosome positioning, and transcription. We identified that H1 was most enriched in transposons. H1 was also found in genes at a lower level compared to transposons, and the abundance of H1 was anticorrelated with gene expression. Moreover, H1 influences nucleosome positioning by increasing the distance between two nucleosomes. Lack of H1 resulted in increased DNA methylation of transposons with heterochromatic features. In contrast, an h1 mutant showed a reduction of DNA methylation in genes and transposons with euchromatic features. Our finding suggests that H1 has a dual function in regulating DNA methylation. That is, H1 inhibits both DNA methyltransferases and DNA demethylation-associated enzymes from binding heterochromatin and euchromatin, respectively. In addition, the hypermethylated loci in our h1 mutant almost perfectly overlapped with the hypomethylated loci in a ddm1 mutant in heterochromatin, suggesting a link between these two proteins. DDM1 is an Snf2 chromatin remodeler that can slide nucleosomes along DNA and has been proposed to provide DNA methyltransferase access to target sequences. We further determined their functional relationship by crossing h1 and ddm1 mutants, and generated a map of DNA methylation of the cross. We identified that loss of DNA methylation from ddm1 was partially recovered by removing H1. Also the mutant phenotype observed in ddm1 disappeared in h1ddm1. Based on our results, we proposed a model where DDM1-mediated chromatin destabilization releases H1 binding, which in turn increases DNA accessibility. It is noteworthy that DNA demethylation preferentially occurred in euchromatin in both the rice seed DNA methylation study and the H1 study. Based on this result, we proposed that the apparent target preference of DNA demethylation-associated proteins depends on the underlying chromatin structure. We think that this chromatin structure-mediated specificity also dictates other nucleoproteins to determine/recognize their targets. My dissertation work tackled multiple aspects of chromatin biology: tissue-specific chromatin regulation, and the interplay between chromatin components in chromatin organization. Together, the results from my work enhanced our knowledge of how chromatin components influence overall chromatin structure.

Download or read book Chromatin Regulation and Dynamics written by Anita Göndör and published by Academic Press. This book was released on 2016-10-25 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chromatin Regulation and Dynamics integrates knowledge on the dynamic regulation of primary chromatin fiber with the 3D nuclear architecture, then connects related processes to circadian regulation of cellular metabolic states, representing a paradigm of adaptation to environmental changes. The final chapters discuss the many ways chromatin dynamics can synergize to fundamentally contribute to the development of complex diseases. Chromatin dynamics, which is strategically positioned at the gene-environment interface, is at the core of disease development. As such, Chromatin Regulation and Dynamics, part of the Translational Epigenetics series, facilitates the flow of information between research areas such as chromatin regulation, developmental biology, and epidemiology by focusing on recent findings of the fast-moving field of chromatin regulation. Presents and discusses novel principles of chromatin regulation and dynamics with a cross-disciplinary perspective Promotes crosstalk between basic sciences and their applications in medicine Provides a framework for future studies on complex diseases by integrating various aspects of chromatin biology with cellular metabolic states, with an emphasis on the dynamic nature of chromatin and stochastic principles Integrates knowledge on the dynamic regulation of primary chromatin fiber with 3D nuclear architecture, then connects related processes to circadian regulation of cellular metabolic states, representing a paradigm of adaptation to environmental changes

Download or read book Epigenetic Gene Expression and Regulation written by Suming Huang and published by Academic Press. This book was released on 2015-10-19 with total page 484 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

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

Download or read book Epigenetic Contributions in Autoimmune Disease written by Esteban Ballestar and published by Springer. This book was released on 2011-08-23 with total page 182 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on the relevance of epigenetic mechanisms in autoimmune disease. It provides new directions for future research in autoimmune disease.

Download or read book Epigenetic Mechanisms of Gene Regulation written by Vincenzo E. A. Russo and published by . This book was released on 1996 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Chromatin Structure and Gene Expression written by Sarah C. R. Elgin and published by Frontiers in Molecular Biology. This book was released on 2000 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since publication of the first edition in 1995, there have been significant advances and understanding of chromatin structure and its relation to gene expression. These include a high-resolution structure of the nucleosome core, discovery of the enzymes and complexes that mediate histone acetylation and deacetylation, discovery of novel ATP-dependent chromatin remodeling complexes, new insights into nuclear organization and epigenetic silencing mechanisms. In light of these advances, Chromatin Structure and Gene Expression (2ed.) includes updated chapters and additional material that introduce new concepts in the process of gene regulation in chromatin.

Download or read book RNA Chromatin Interactions written by Ulf Andersson Vang Ørom and published by Humana. This book was released on 2020-07-18 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on RNAs interacting with chromatin and their function. Chapters guide readers through transcription, splicing, non-coding RNA function and manipulation of gene expression. 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. Authoritative and cutting-edge, RNA-Chromatin Interactions: Methods and Protocols aims to be a starting-point to expand researchers experimental approaches towards the numerous outstanding questions in this new and expanding field.

Download or read book The Structure and Function of Chromatin written by David W. FitzSimons and published by John Wiley & Sons. This book was released on 2009-09-16 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Novartis Foundation Series is a popular collection of the proceedings from Novartis Foundation Symposia, in which groups of leading scientists from a range of topics across biology, chemistry and medicine assembled to present papers and discuss results. The Novartis Foundation, originally known as the Ciba Foundation, is well known to scientists and clinicians around the world.

Download or read book Nuclear Dynamics written by K. Nagata and published by Springer Science & Business Media. This book was released on 2007-12-03 with total page 285 pages. Available in PDF, EPUB and Kindle. Book excerpt: The dynamics of nuclear structures described in this book furnish the basis for a comprehensive understanding of how the higher-order organization and function of the nucleus is established and how it correlates with the expression of a variety of vital activities such as cell proliferation and differentiation. The resulting volume creates an invaluable source of reference for researchers in the field.

Download or read book Nuclear Architecture and Dynamics written by Christophe Lavelle and published by Academic Press. This book was released on 2017-10-27 with total page 620 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nuclear Architecture and Dynamics provides a definitive resource for (bio)physicists and molecular and cellular biologists whose research involves an understanding of the organization of the genome and the mechanisms of its proper reading, maintenance, and replication by the cell. This book brings together the biochemical and physical characteristics of genome organization, providing a relevant framework in which to interpret the control of gene expression and cell differentiation. It includes work from a group of international experts, including biologists, physicists, mathematicians, and bioinformaticians who have come together for a comprehensive presentation of the current developments in the nuclear dynamics and architecture field. The book provides the uninitiated with an entry point to a highly dynamic, but complex issue, and the expert with an opportunity to have a fresh look at the viewpoints advocated by researchers from different disciplines. Highlights the link between the (bio)chemistry and the (bio)physics of chromatin Deciphers the complex interplay between numerous biochemical factors at task in the nucleus and the physical state of chromatin Provides a collective view of the field by a large, diverse group of authors with both physics and biology backgrounds

Download or read book Epigenetics and Regeneration written by and published by Academic Press. This book was released on 2019-05-24 with total page 541 pages. Available in PDF, EPUB and Kindle. Book excerpt: Epigenetics and Regeneration compiles the first foundational reference on epigenetic mechanisms governing tissue development, repair, homeostasis, and regeneration, as well as pathways to employ these mechanisms in clinical practice and translational science. In this book, life science researchers, clinicians, and students will discover an interdisciplinary resource bringing together common themes in the field, background overviews, research methods, recent advances, and opportunities for drug discovery. Throughout this volume, special attention is paid to pre-clinical and first clinical studies aimed at increasing the regenerative potential of damaged tissues by epigenetic drugs, as well as innovative, discipline spanning strategies to enhance cell reprogramming. As an all-inclusive, evidence-based volume, Epigenetics and Regeneration will stimulate discussion and boost new research in this fascinating and impactful area of translational epigenetics. Provides a foundational overview of epigenetics in regenerative medicine Examines epigenetic components of tissue regeneration for a variety of organ systems and tissue types, as well as current attempts to employ these mechanisms in clinical practice Offers researchers, students, clinicians, and pharmacologists the tools they need to enhance tissue development, repair, homeostasis, and regeneration and explore new epigenetic therapeutic pathways Features chapter contributions from leading international researchers and clinicians in the fields of epigenetics and regenerative medicine

Download or read book Chromatin and Disease written by Tapas K. Kundu and published by Springer Science & Business Media. This book was released on 2007-05-04 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book includes a collection of articles with the broad theme of disease connection to chromatin structure and function. It elaborates on the molecular pharmacology of the drugs targeting chromatin structure and its components. The book contains up-to-date information about the chromatin structure and chromatin related diseases and drug functions. This work is the first endeavor to present different aspects encompassing the above theme.

Download or read book The Nucleolus written by Mark O. J. Olson and published by Springer Science & Business Media. This book was released on 2011-09-15 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: Within the past two decades, extraordinary new functions for the nucleolus have begun to appear, giving the field a new vitality and generating renewed excitement and interest. These new discoveries include both newly-discovered functions and aspects of its conventional role. The Nucleolus is divided into three parts: nucleolar structure and organization, the role of the nucleolus in ribosome biogenesis, and novel functions of the nucleolus.

Download or read book Nuclear Organization and Function written by Terri Grodzicker and published by . This book was released on 2011 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is based on presentations by the world-renowned investigators who gathered at the 75th annual Cold Spring Harbor Symposium on Quantitative Biology to discuss the organization and function of the cell nucleus. It reviews the latest advances in research into nuclear structure, the organization of the genome within the nucleus, and spatiotemporal coordination of nuclear processes. The topics examined include nuclear domains, chromatin organization, transcription and RNA processing, DNA replication, nuclear reprogramming, and epigenetics. Cancer, premature aging syndromes, and other diseases that may be associated with altered nuclear organization are also covered.

Download or read book Mechanisms of Gene Regulation written by Carsten Carlberg and published by Springer. This book was released on 2016-06-06 with total page 219 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook aims to describe the fascinating area of eukaryotic gene regulation for graduate students in all areas of the biomedical sciences. Gene expression is essential in shaping the various phenotypes of cells and tissues and as such, regulation of gene expression is a fundamental aspect of nearly all processes in physiology, both in healthy and in diseased states. This pivotal role for the regulation of gene expression makes this textbook essential reading for students of all the biomedical sciences, in order to be better prepared for their specialized disciplines. A complete understanding of transcription factors and the processes that alter their activity is a major goal of modern life science research. The availability of the whole human genome sequence (and that of other eukaryotic genomes) and the consequent development of next-generation sequencing technologies have significantly changed nearly all areas of the biological sciences. For example, the genome-wide location of histone modifications and transcription factor binding sites, such as provided by the ENCODE consortium, has greatly improved our understanding of gene regulation. Therefore, the focus of this book is the description of the post-genome understanding of gene regulation. The purpose of this book is to provide, in a condensed form, an overview on the present understanding of the mechanisms of gene regulation. The authors are not aiming to compete with comprehensive treatises, but rather focus on the essentials. Therefore, the authors have favored a high figure-to-text ratio following the rule stating that “a picture tells more than thousand words”. The content of the book is based on the lecture course, which is given by Prof. Carlberg since 2001 at the University of Eastern Finland in Kuopio. The book is subdivided into 4 sections and 13 chapters. Following the Introduction there are three sections, which take a view on gene regulation from the perspective of transcription factors, chromatin and non-coding RNA, respectively. Besides its value as a textbook, Mechanisms of Gene Regulation will be a useful reference for individuals working in biomedical laboratories.

Download or read book Epigenetics Nuclear Organization Gene Function written by John C. Lucchesi and published by Oxford University Press. This book was released on 2018-12-19 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: Epigenetics is the study of heritable changes in gene function that do not involve changes in the DNA sequence. These changes, consisting principally of DNA methylation, histone modifications, and non-coding RNAs, maintain or modulate the initial impact of regulatory factors that recognize and associate with particular genomic sequences. Epigenetic modifications are manifest in all aspects of normal cellular differentiation and function, but they can also have damaging effects that result in pathologies such as cancer. Research is continuously uncovering the role of epigenetics in a variety of human disorders, providing new avenues for therapeutic interventions and advances in regenerative medicine. This book's primary goal is to establish a framework that can be used to understand the basis of epigenetic regulation and to appreciate both its derivation from genetics and interdependence with genetic mechanisms. A further aim is to highlight the role played by the three-dimensional organization of the genetic material itself (the complex of DNA, histones and non-histone proteins referred to as chromatin), and its distribution within a functionally compartmentalized nucleus. This architectural organization of the genome plays a major role in the subsequent retrieval, interpretation, and execution of both genetic and epigenetic information.