Chromatin Regulation and Dynamics

Chromatin Regulation and Dynamics
Author: Anita Göndör
Publsiher: Academic Press
Total Pages: 496
Release: 2016-10-25
Genre: Science
ISBN: 9780128034026

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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

Chromatin
Author: Ralf Blossey
Publsiher: CRC Press
Total Pages: 172
Release: 2017-08-04
Genre: Medical
ISBN: 9781351646819

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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.

Chromatin Stability and Dynamics Targeting and Recruitment of Chromatin Modifiers

Chromatin Stability and Dynamics  Targeting and Recruitment of Chromatin Modifiers
Author: Sara Farrona,Rafal Archacki,Juan Armando Casas-Mollano,Iva Mozgová
Publsiher: Frontiers Media SA
Total Pages: 135
Release: 2021-07-27
Genre: Science
ISBN: 9782889710911

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Chromatin

Chromatin
Author: Ralf Blossey
Publsiher: CRC Press
Total Pages: 172
Release: 2017-08-04
Genre: Computers
ISBN: 9781498729383

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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.

Chromatin Regulation in Cell Fate Decisions

Chromatin Regulation in Cell Fate Decisions
Author: José Luis Sardina,Justin Brumbaugh,Bruno Di Stefano
Publsiher: Frontiers Media SA
Total Pages: 135
Release: 2021-10-20
Genre: Science
ISBN: 9782889715107

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Investigating the Roles of Histone Residues Chaperones and Modifiers in Chromatin Regulation Chromatin Dynamics and DNA Excision Repair

Investigating the Roles of Histone Residues  Chaperones  and Modifiers in Chromatin Regulation  Chromatin Dynamics  and DNA Excision Repair
Author: Amelia J. Hodges
Publsiher: Unknown
Total Pages: 284
Release: 2017
Genre: Electronic Book
ISBN: OCLC:1057284841

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In a eukaryotic cell, DNA is packaged into chromatin, a highly dynamic and highly regulated structure. Chromatin is composed of nucleosome subunits, comprised of an octamer of histone proteins wrapped by DNA. Histone proteins are highly conserved among species, and also show a high degree of post-translational modification. In this work, we sought to better understand the roles of histone residues, histone domains, and histone modification in chromatin regulation and dynamics using Saccharomyces cerevisiae as a model eukaryote. In part one of this dissertation, we examine key residues and domains of histone proteins and how they interact with the cellular environment. First, we determined the "sprocket" arginine residues that project into the minor groove of DNA as it wraps around the histone octamer are important for cell viability, histone occupancy, gene expression and DNA repair. Second, we determined the nucleosome acidic patch that forms a negatively charged surface in the solvent-exposed region of the nucleosome is important for histone occupancy and binding to the essential histone chaperone FACT. Third, we found the histone H2B repression (HBR) domain in the H2B N-terminal tail is important for FACT binding and DNA damage resistance. Collectively, these studies increase our understanding of how unique features in histone structure regulate chromatin structure and interactions. In part two of this dissertation, we examine the roles of essential chromatin-associated factors in response to DNA damage. During the DNA damage response, chromatin must be transiently remodeled in order for DNA repair to occur. However, the roles of specific chromatin factors in the DNA damage response are still being elucidated. We optimized the anchor-away method to conditionally deplete essential chromatin factors from the yeast cell nucleus, and discovered the NuA4 histone acetyltransferase complex plays an important role in DNA excision repair. These studies highlight the role of essential chromatin factors in repairing DNA lesions.

Introduction to Epigenetics

Introduction to Epigenetics
Author: Renato Paro,Ueli Grossniklaus,Raffaella Santoro,Anton Wutz
Publsiher: Springer Nature
Total Pages: 215
Release: 2021-03-23
Genre: Science
ISBN: 9783030686703

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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

Gene Regulation Epigenetics and Hormone Signaling

Gene Regulation  Epigenetics and Hormone Signaling
Author: Subhrangsu S. Mandal
Publsiher: John Wiley & Sons
Total Pages: 656
Release: 2017-05-03
Genre: Science
ISBN: 9783527697250

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The first of its kind, this reference gives a comprehensive but concise introduction to epigenetics before covering the many interactions between hormone regulation and epigenetics at all levels. The contents are very well structured with no overlaps between chapters, and each one features supplementary material for use in presentations. Throughout, major emphasis is placed on pathological conditions, aiming at the many physiologists and developmental biologists who are familiar with the importance and mechanisms of hormone regulation but have a limited background in epigenetics.

Chromatin and Disease

Chromatin and Disease
Author: Tapas K. Kundu,Dipak Dasgupta
Publsiher: Springer Science & Business Media
Total Pages: 458
Release: 2007-05-04
Genre: Science
ISBN: 9781402054662

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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.

The Regulation of Chromatin Dynamics by Histone Chaperones and Variants

The Regulation of Chromatin Dynamics by Histone Chaperones and Variants
Author: Rachel Miriam Zunder
Publsiher: Unknown
Total Pages: 258
Release: 2011
Genre: Electronic Book
ISBN: OCLC:858268734

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In all eukaryotic organisms, DNA is packaged into chromatin, which controls gene expression and genomic stability. The chromatin landscape is dynamic and responds to environmental signals to direct different cellular programs. Chromatin architecture is regulated by a network of structural and enzymatic proteins that interact with histones to alter nucleosome composition. In my dissertation, I examined 1) the interaction between histone chaperones and newly synthesized histones during nucleosome assembly and 2) the interplay between canonical histone isotypes, histone variants, and histone modifications. My work established how the unusual domain architecture of a newly discovered histone chaperone, Rtt106, provides specificity for acetylated histone cargo. Additionally, I discovered several new histone modifications and examined the relationship between the histone variant H2A.Z and two canonical histone H2B isotypes (Htb1 and Htb2). My dissertation establishes a framework for understanding the additional levels of genomic regulation achieved by histone chaperones, variants, isotypes, and modifications. In chapter 2, I examine the structural basis for the specificity of the histone chaperone Rtt106 for H3 molecules modified by an acetylation at lysine 56 (H3K56ac). The X ray crystal structure, determined by our collaborators Andy Antczak and James Berger, revealed that Rtt106 contains a double pleckstrin homology (PH) motif. A targeted mutational screen identified two regions on Rtt106 that, when mutated individually, each disrupted Rtt106-H3 binding. One region was a basic surface on the N-terminal PH domain and the other was a loop within the C-terminal PH domain. Although binding experiments did not directly identify an H3K56ac binding pocket on Rtt106, a comparative analysis with the chromatin remodeling protein Pob3 implicated the C-terminal loop as the source of H3K56ac-specificity in the Rtt106-H3 interaction. This work establishes new domain architecture for acetyl-lysine recognition and expands our understanding of how chaperone-histone binding is regulated. Armed with Rtt106 mutants that reduced H3 binding activity, in chapter 3 I examine the role of Rtt106-mediated nucleosome assembly during replication, transcription, and silencing. Although Rtt106 mutant proteins localized to origins of replication and silent chromatin, without the ability to bind H3, these mutants could not deliver H3K56ac into chromatin. Reduced H3K56ac occupancy was detrimental to replication whereas excess unincorporated H3K56ac was antagonistic to silencing. In contrast, H3K56ac binding was required to recruit Rtt106 to histone gene promoters. Without recruitment of Rtt106 to these loci, we observed defects in H3K56ac incorporation and histone gene repression. Our work demonstrates that Rtt106-H3 binding is necessary for all known branches Rtt106-mediated nucleosome assembly, however these different branches rely on distinct genomic localization cues to target Rtt106 to chromatin. To analyze the relationships between canonical histones, modifications, and variants, in chapter 4 I explore the unique functions of two histone H2B isotypes, Htb1 and Htb2. In collaboration with the Freitas lab at the Ohio State University, we discovered three new modifications on H2B, one of which was isotype-specific. Although the dimeric association of H2A.Z with H2B did not reveal an isotype-specific interaction, the interplay between canonical histone isotypes and variants remains an intriguing paradigm for chromatin regulation. In collaboration with the Giaever lab at the University of Toronto, we used chemical genomic profiling to define unique functions associated with the Htb1 and Htb2 isotypes. However, all chemical sensitivities identified resulted from changes in histone expression rather than Htb1 and Htb2 protein activity. Although we are still searching for a functional distinction between the two H2B isotypes, mass spectrometry analyses coupled with chemical-genomic profiling represents a promising strategy for discovering these relationships and defining their functional impact.

Plant Chromatin Dynamics

Plant Chromatin Dynamics
Author: Marian Bemer,Célia Baroux
Publsiher: Humana Press
Total Pages: 659
Release: 2017-10-20
Genre: Science
ISBN: 1493973177

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This volume provides a comprehensive collection of protocols that can be used to study plant chromatin structure and composition. Chapters divided into three sections detail the profiling of chromatin features in relation to epigenetic regulation, investigate the interaction between chromatin modifications and gene regulation, and explore the 3D spatial organization of the chromatin inside the nucleus. 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, Plant Chromatin Dynamics: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Epigenetic Gene Expression and Regulation

Epigenetic Gene Expression and Regulation
Author: Suming Huang,Michael D Litt,C. Ann Blakey
Publsiher: Academic Press
Total Pages: 482
Release: 2015-10-19
Genre: Science
ISBN: 9780128004715

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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

Chromatin and Epigenetics

Chromatin and Epigenetics
Author: Colin Logie,Tobias Aurelius Knoch
Publsiher: BoD – Books on Demand
Total Pages: 294
Release: 2020-01-29
Genre: Science
ISBN: 9781789844924

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Genomics has gathered broad public attention since Lamarck put forward his top-down hypothesis of 'motivated change' in 1809 in his famous book "Philosophie Zoologique" and even more so since Darwin published his famous bottom-up theory of natural selection in "The Origin of Species" in 1859. The public awareness culminated in the much anticipated race to decipher the sequence of the human genome in 2002. Over all those years, it has become apparent that genomic DNA is compacted into chromatin with a dedicated 3D higher-order organization and dynamics, and that on each structural level epigenetic modifications exist. The book "Chromatin and Epigenetics" addresses current issues in the fields of epigenetics and chromatin ranging from more theoretical overviews in the first four chapters to much more detailed methodologies and insights into diagnostics and treatments in the following chapters. The chapters illustrate in their depth and breadth that genetic information is stored on all structural and dynamical levels within the nucleus with corresponding modifications of functional relevance. Thus, only an integrative systems approach allows to understand, treat, and manipulate the holistic interplay of genotype and phenotype creating functional genomes. The book chapters therefore contribute to this general perspective, not only opening opportunities for a true universal view on genetic information but also being key for a general understanding of genomes, their function, as well as life and evolution in general.

Chromatin Structure and Dynamics

Chromatin Structure and Dynamics
Author: J. Zlatanova,S. H. Leuba
Publsiher: Gulf Professional Publishing
Total Pages: 507
Release: 2004
Genre: Science
ISBN: 0444515941

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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.

Nuclear Dynamics

Nuclear Dynamics
Author: K. Nagata,K. Takeyasu
Publsiher: Springer Science & Business Media
Total Pages: 279
Release: 2007-12-03
Genre: Science
ISBN: 9784431301301

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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.