ATP-dependent Nucleosome Mobilization in the Presence of Proteins Involved in Transcriptional Silencing


Book Description

Recruitment of the yeast Silencing Information Regulator complex (SIR complex) to regions of silenced heterochromatin is essential for maintaining a transcriptionally-repressed chromatin environment. Distinct boundaries exist to demarcate silenced heterochromatin from facultative heterochromatin and yet little is known regarding how this boundary is established or maintained. In this study, we observed linker DNA-independent binding of Sir3 to the nucleosome. We then examined the interactions of Sir3 with the ATP-dependent chromatin remodeling complexes ISW2, ISW1a, INO80, ISW1b, and SWI/SNF. In the cell, the interplay between these remodeling complexes, the SIR complex, and other chromatin associated proteins likely plays a regulatory function to maintain silencing throughout a particular region and restrict the spreading of this silenced state to adjacent chromatin regions. Investigations of the silent mating type locus in yeast may provide important clues toward understanding global transcriptional silencing mechanisms in higher eukaryotes. We demonstrate that Sir3 has no inhibitory effect upon remodeling by any of the complexes examined in this study and that Sir3 does not prevent ISW2 or SWI/SNF from binding the nucleosome.







Replication and Transcription of Chromatin


Book Description

Replication and Transcription of Chromatin summarizes the main structural features of chromatin and presents results on replication and transcription gained over the last 20 years. The book emphasizes DNA-histone complexes and their importance in restricting genetic information encoded in DNA. Figures are used to illustrate many of the most important concepts of chromatin replication and transcription, and promising hypotheses and models are discussed to promote further research. Replication and Transcription of Chromatin is an important reference for biochemists, biophysicists, molecular biologists, cell biologists, and other researchers interested in this topic.




Chromatin Structure and Gene Expression


Book Description

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.




Translating Epigenetics to the Clinic


Book Description

Translating Epigenetics to the Clinic reviews current methodological tools and experimental approaches used by leading translational researchers seeking to use epigenetics as a clinical model. It organizes epigenetics into disease treatment areas with a major focus on oncology, and with much coverage of pervasive treatment categories such as diabetes, as well as the ‘diseases of modernity’—including pharmacological addiction, dementia, and ageing. Pedagogically, the work concentrates on the latest knowledge, laboratory techniques, and experimental approaches used by translational research leaders in this field. The book promotes cross-disciplinary communication between the sub-specialties of medicine. In common with the rest of the books in Translational Medicine, the book remains unified in theme by emphasizing recent innovations, critical barriers to progress, and the new tools being used to overcome them. Also includes specific areas of research that require additional study to advance the field as a whole. Encompasses the latest innovations and tools being used to apply epigenetics in the lab and clinic Features extensive pedagogical updates aiming to improve the education of translational researchers in this field Offers a transdisciplinary approach to support cross-fertilization between different sub-specialties of medicine




Nuclear Hormone Receptors


Book Description

An overview of the supergene family made up of those nuclear hormone receptors which recognize thyroid and steroid hormones, vitamen D and retinoic acid and which are characterized by their ability to bind both ligands and the genes which respond to them.




Histone Deacetylases


Book Description

A panel of leading investigators summarizes and synthesizes the new discoveries in the rapidly evolving field of histone acetylation as a key regulatory mechanism for gene expression. The authors describe what has been learned about these proteins, including the identification of the enzymes, the elucidation of the enzymatic mechanisms of action, and the identification of their substrates and their partners. They also review the structures that have been solved for a number of enzymes-both alone and in complex with small molecule inhibitors-and the biological roles of the several histone deacetylases (HDAC) genes that have been knocked out in mice.




Fundamentals of Chromatin


Book Description

​​​​​​​​​​​​​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.




The Nucleus, Second Edition


Book Description

The nucleus is the most prominent structure in eukaryotic cells. It houses the cell's DNA and is the hub for DNA replication, transcription, and RNA processing. Despite its prominence and importance, our understanding of how the nucleus and its DNA are organized in space and time--and the implications of that organization for proper function--has lagged behind that of other cellular structures. Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Biology covers recent advances in our understanding of nuclear organization and function. The contributors discuss the 3D organization of chromatin, the various nuclear bodies and compartments that have been identified, and the roles of RNA and actin in shaping nuclear organization, as well as how these structures interact with each other and with peripheral features (e.g., the nuclear pore complex and inner nuclear membrane proteins) to carry out the work of the nucleus. Insights into DNA replication timing and RNA processing dynamics based on new technologies aimed at examining chromatin and other intranuclear structures at high resolution are also included. Multiple chapters are devoted to physiological and disease processes involving disruption of nuclear structure and function (e.g., viral infection). This volume is therefore essential reading for all cell and molecular biologists, as well as pathologists interested in the role of nuclear architecture in disease.




Encyclopedia of Cell Biology


Book Description

The Encyclopedia of Cell Biology, Four Volume Set offers a broad overview of cell biology, offering reputable, foundational content for researchers and students across the biological and medical sciences. This important work includes 285 articles from domain experts covering every aspect of cell biology, with fully annotated figures, abundant illustrations, videos, and references for further reading. Each entry is built with a layered approach to the content, providing basic information for those new to the area and more detailed material for the more experienced researcher. With authored contributions by experts in the field, the Encyclopedia of Cell Biology provides a fully cross-referenced, one-stop resource for students, researchers, and teaching faculty across the biological and medical sciences. Fully annotated color images and videos for full comprehension of concepts, with layered content for readers from different levels of experience Includes information on cytokinesis, cell biology, cell mechanics, cytoskeleton dynamics, stem cells, prokaryotic cell biology, RNA biology, aging, cell growth, cell Injury, and more In-depth linking to Academic Press/Elsevier content and additional links to outside websites and resources for further reading A one-stop resource for students, researchers, and teaching faculty across the biological and medical sciences