chromatin regulation and dynamics

Chromatin Regulation And Dynamics
Author: Anita Göndör
Publisher: Academic Press
Release Date: 2016-10-25
Pages: 496
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

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

Chromatin
Author: Ralf Blossey
Publisher: CRC Press
Release Date: 2017-08-04
Pages: 172
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

An invaluable resource for computational biologists and researchers from other fields seeking an introduction to the topic, Chromatin: Structure, Dynamics, Regulation offers comprehensive coverage of this dynamic interdisciplinary field, from the basics to the latest research. Computational methods from statistical physics and bioinformatics are detailed whenever possible without lengthy recourse to specialized techniques.

Using Chromatin Dynamics To Understand Transcriptional Regulation And Genetic Variance
Author: Samantha Nicole Piekos
Publisher:
Release Date: 2020
Pages:
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

The genome is the same in every cell of an organism, but complex organisms have multiple cell types. This is due to the epigenome specifying a cell's transcriptional state resulting in distinct cell identities. Despite 98.5% of the human genome is non-coding and the site of epigenomic activity, which specifies instructions for regulating transcription of the coding region, relatively little is known about its function. A major hurdle with studying non-coding regulatory elements is identifying their distal gene and regulatory targets. Here, I solve this issue by using the three-dimensional chromatin conformation to identify targets that are in close physical proximity of the regulatory element. By integrating data on the three-dimensional chromatin state with other epigenomic measures including the open chromatin regions, transcription factor binding sites, and histone modifications I provide genome-wide insight into how the epigenome establishes the transcriptional state of the cell. In addition, I have developed a new method for prioritizing non-coding genetic variants in complex phenotypes. I validated this method in the context of Type 1 Diabetes and craniofacial disorders. In this dissertation, I demonstrate how data integration of multiple measurements of the epigenome and transcriptome provides insight into methods of transcriptional regulation and how this regulation is influenced by genetic variance.

Plant Chromatin Dynamics
Author: Célia Baroux
Publisher:
Release Date: 2018
Pages: 659
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

Stem Cell Proliferation And Differentiation
Author: Thomas Fazzio
Publisher: Academic Press
Release Date: 2020-04
Pages: 362
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

Stem Cell Proliferation and Differentiation, Volume 138, the latest release in the Current Topics in Developmental Biology series, highlights new advances in the field, with this new volume presenting interesting chapters. Each chapter is written by an international board of authors.

Nuclear Dynamics
Author: K. Nagata
Publisher: Springer Science & Business Media
Release Date: 2007-12-03
Pages: 279
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

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.

Epigenetic Gene Expression And Regulation
Author: Suming Huang
Publisher: Academic Press
Release Date: 2015-10-19
Pages: 482
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

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

Transcriptional And Chromatin Regulation In Adaptive And Innate Immune Cells
Author: Keiko Ozato
Publisher: Frontiers Media SA
Release Date: 2020-05-22
Pages:
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

Transcription depends on an ordered sequence of events, starting with (i) setting of the enhancer and chromatin environment, (ii) assembly of DNA binding and general transcription factors, (iii) initiation, elongation, processing of mRNA and termination, followed by (iv) creation of epigenetic marks and memory formation. Highlighting the importance of these activities, more than 10% total genes are dedicated to regulating transcriptional mechanisms. This area of research is highly active and new insights are continuously being added to our knowledge. Cells of the immune system have unique features of gene regulation to support diverse tasks required for innate and adaptive immunity. Innate immunity involves the recognition of external infectious and noxious agents as well as internal cancer cell components, and the elimination of these agents by non-specific mechanisms. Adaptive immunity involves gene rearrangement to achieve highly specific T and B cell responses, imparting the capability of self and non-self discrimination. This requires transcription and epigenetic regulation. Adaptive immunity also employs epigenetic memory, enabling recapitulation of prior transcription. Recent advances in nuclear architecture, chromatin structure, and transcriptional regulation have provided new insights into immune responses. The increased understanding of these molecular mechanisms is now affording opportunities to improve therapeutic strategies for various diseases.

Chromatin And Disease
Author: Tapas K. Kundu
Publisher: Springer Science & Business Media
Release Date: 2007-05-04
Pages: 458
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

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.

Understanding Immunobiology Through The Specificity Of NF   B
Author: Myong-Hee Sung
Publisher: Frontiers Media SA
Release Date: 2020-02-20
Pages:
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

Chromatin Structure And Dynamics
Author: J. Zlatanova
Publisher: Gulf Professional Publishing
Release Date: 2004
Pages: 507
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

Biological processes that replicate, preserve and use the genetic information encoded in DNA must operate in the context of chromatin, a highly organized complex of DNA and proteins. These proteins do not merely package the DNA in the tiny volume of the nucleus, but impart the structure the ability to change according to the requirements of the specific process the DNA is involved in. Moreover, chromatin structure is used by the cell to control the activity of DNA. In this volume the basics of chromatin structure and dynamics are presented by established experts in the field.

Developing Computational And Experimental Tools To Understand Chromatin Dynamics And Regulation
Author: Linfeng Yang
Publisher:
Release Date: 2020
Pages:
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

The human genome is condensed yet accessible, allowing cells to execute complex logic needed for cellular programs. The dynamic physical organization of the genome is connected to its instantaneous transcriptional profile. Current sequencing technologies can only recover a static and highly-averaged picture of these dynamic processes. Identification of dynamic signatures from chromatin motion requires an imaging and analysis platform for simultaneous tracking of genes and their transcriptional state in live cells. Advances in microscopy have provided a great opportunity to obtain such information. Unfortunately, segmenting overlapping nuclei is still a major challenge for single cell microscopic measurement. We first reported a deep-learning based model 'Nuclear Segmentation Tool' (NuSeT) that accurately segments multiple types of nuclei from imaging data. Using a hybrid architecture that consists of U-Net and Region Proposal Networks (RPN), followed by watershed processing, NuSeT has achieved superior performance in delineating nuclear boundaries in images of varying complexities. NuSeT further improves nuclear detection and reduces false positives by employing foreground normalization and additional training on synthetic images containing non-cellular artifacts. NuSeT also addresses common bottlenecks in nuclear segmentation such as limited training samples, variability in nuclear signal and shapes, and sample preparation artifacts. NuSeT consistently fares better in generating accurate segmentation masks and assigning boundaries for touching nuclei compared with other state-of-the-art segmentation models. Next, we developed an imaging platform for simultaneous real-time visualization of locus dynamics and transcriptional output. Using a CRISPR/Cas9 based gene knock-in strategy, we have introduced MS2 hairpin cassettes into native genes of interest, which can reveal their transcriptional states. To track these loci for extended periods of time at high spatiotemporal resolution, we have generated optical tag ArrayG/N fusions of the nuclease deactivated Cas9 (dCas9) and a polycistronic cassette of repeating tRNA-sgRNA delivered by lentivirus. This platform enables sustainable tracking of non-repetitive genomic loci. We have further modified ArrayG/N tags to recruit chromatin effectors at selected genomic sites that makes this experimental platform particularly well suited for dynamic monitoring of epigenetic manipulations on selected genes. Using this platform, we have measured dynamic signatures of chromatin accessibility. We have also shown that the motion of gene loci are further constrained when they are transcriptionally active. These image analysis and cellular engineering tools can be used to answer other outstanding questions about the chromatin and gene regulation dynamics.

Nuclear Architecture And Dynamics
Author: Christophe Lavelle
Publisher: Academic Press
Release Date: 2017-10-27
Pages: 618
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

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

Plant Transposons And Genome Dynamics In Evolution
Author: Nina V. Fedoroff
Publisher: John Wiley & Sons
Release Date: 2013-01-16
Pages: 232
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

The transposable genetic elements, or transposons, as they are now known, have had a tumultuous history. Discovered in the mid-20th century by Barbara McClintock, they were initially received with puzzlement. When their genomic abundance began to be apparent, they were categorized as "junk DNA" and acquired the label of parasites. Expanding understanding of gene and genome organization has revealed the profound extent of their impact on both. Plant Transposons and Genome Dynamics in Evolution captures and distills the voluminous research literature on plant transposable elements and seeks to assemble the big picture of how transposons shape gene structure and regulation, as well as how they sculpt genomes in evolution. Individual chapters provide concise overviews of the many flavors of plant transposons and of their roles in gene creation, gene regulation, development, genome evolution, and organismal speciation, as well as of their epigenetic regulation. This volume is essential reading for anyone working in plant genetics, epigenetics, or evolutionary biology.

Epigenetic Regulation And Epigenomics
Author: Robert A. Meyers
Publisher: John Wiley & Sons
Release Date: 2012-10-02
Pages: 1254
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

Epigenetics is a term in biology referring to heritable traits that do not involve changes in the underlying DNA sequence of the organism. Epigenetic traits exist on top of or in addition to the traditional molecular basis for inheritance. The "epigenome" is a parallel to the word "genome," and refers to the overall epigenetic state of a cell. Cancer and stem cell research have gradually focused attention on these genome modifications. The molecular basis of epigenetics involves modifications to DNA and the chromatin proteins that associate with it. Methylation, for example, can silence a nearby gene and seems to be involved in some cancers. Epigenetics is beginning to form and take shape as a new scientific discipline, which will have a major impact on Medicine and essentially all fields of biology. Increasingly, researchers are unearthing links between epigenetics and a number of diseases. Although in recent years cancer has been the main focus of epigenetics, recent data suggests that epigenetic plays a critical role in psychology and psychopathology. It is being realized that normal behaviors such as maternal care and pathologies such as Schizophrenia and Alzheimer's might have an epigenetic basis. It is also becoming clear that nutrition and life experiences have epigenetic consequences. Discover more online content in the Encyclopedia of Molecular Cell Biology and Molecular Medicine.

Fundamentals Of Chromatin
Author: Jerry L. Workman
Publisher: Springer Science & Business Media
Release Date: 2013-12-04
Pages: 587
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

​​​​​​​​​​​​​While there has been an increasing number of books on various aspects of epigenetics, there has been a gap over the years in books that provide a comprehensive understanding of the fundamentals of chromatin. ​Chromatin is the combination of DNA and proteins that make up the genetic material of chromosomes. Its primary function is to package DNA to fit into the cell, to strengthen the DNA to prevent damage, to allow mitosis and meiosis, and to control the expression of genes and DNA replication. The audience for this book is mainly newly established scientists ​and graduate students. Rather than going into the more specific areas of recent research on chromatin the chapters in this book give a strong, updated groundwork about the topic. Some the fundamentals that this book will cover include the structure of chromatin and biochemistry and the enzyme complexes that manage it.

Protein Complexes That Modify Chromatin
Author: Jerry L. Workman
Publisher: Springer Science & Business Media
Release Date: 2003-01-08
Pages: 298
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

An early view of eukaryotic chromosomes was that of static structures, which stored DNA not in use within a given cell type. It was thought that packaging of DNA into higher levels of chromatin structure would suffice to repress gene expression and that the challenge to the cell would be to rescue specific sequences from these structures. The exten sive packaging of inactive DNA was considered the primary difference between eukaryotic and prokaryotic genomes and except for that point both would be similarly regulated by cis-acting sequences and trans acting factors. Our view of eukaryotic chromosomes has evolved dra matically over the last decade. The picture of chromosomes that is emerging is that of dynamic breathing organelles actively regulating the flow of genetic information from the genome. Indeed chromatin is so fluid that even maintaining gene quiescence is an active process and is tightly regulated. Chromatin dynamics is a consequence of protein complexes that modify histones, remove histone modifications, mobi lize nucleosomes or stabilize nucleosomes. Awide variety of such com plexes have now been described. Some are abundant and may play glo bal roles in chromosome fluidity and function. Others are more rare and specialized for specific functions at discreet loci. Moreover, several complexes share biochemical activities and genetic studies suggest overlapping functions in vivo. Many components of these complexes were first revealed in genetic screens, while others were discovered by novel cell biological or biochemical approaches.

Encyclopedia Of Biological Chemistry
Author:
Publisher: Academic Press
Release Date: 2013-01-08
Pages: 3232
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

The 4-volume Encyclopedia of Biological Chemistry, Second Edition, represents the current state of a dynamic and crucial field of study. The Encyclopedia pulls together over 500 articles that help define and explore contemporary biochemistry, with content experts carefully chosen by the Editorial Board to assure both breadth and depth in its coverage. Editors-In-Chief William J. Lennarz and M. Daniel Lane have crafted a work that proceeds from the acknowledgement that understanding every living process-from physiology, to immunology, and genetics-is impossible without a grasp on the basic chemistry that provides its underpinning. Each article in the work provides an up-to-date snapshot of a given topic, written by experts, as well as suggestions for further readings for students and researcher wishing to go into greater depth. Available on-line via SciVerse ScienceDirect, the functionality of the Encyclopedia will provide easy linking to referenced articles, electronic searching, as well an online index and glossary to aid comprehension and searchability. This 4-volume set, thoroughly up-to-date and comprehensive, expertly captures this fast-moving field Curated by two esteemed editors-in-chief and an illustrious team of editors and contributors, representing the state of the field Suggestions for further readings offer researchers and students avenues for deeper exploration; a wide-ranging glossary aids comprehension

The Nuclear Pore Complex And Chromatin Domain Dynamics
Author: Guilia Jale Gurun Ruben
Publisher:
Release Date: 2011
Pages: 264
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

Dynamics Of Cell Division
Author: Sharyn A. Endow
Publisher: OUP Oxford
Release Date: 1998-10-01
Pages: 340
ISBN:
Available Language: English, Spanish, And French
EBOOK SYNOPSIS:

This volume focuses on the structural aspects of cell division - concentrating on both nuclear division (meiosis and mitosis) and cytoplasmic division (cytokinesis). Written as a companion volume to the earlier book in the series - Cell Cycle Control, this book provides an up-to-date account of developments in this exciting area of cell biology.