Download or read book The Role of Polycomb Group Proteins in Hox Gene Regulation and Chromatin Organization written by Claudia Gentile and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "Proper embryonic development requires the function of the Hox gene family, which encode transcription factors essential for patterning the developing embryo along its main body axis. Most remarkably, the Hox genes are expressed in a spatially- and temporally- collinear fashion, corresponding to their relative positions along the chromosome. As such, mechanisms for Hox gene activation have been largely studied as the deregulation of Hox genes leads to severe developmental malformations. Our lab uses the developing limb as a model system to study Hox gene regulation. Previous work in our lab as well as others has contributed to understanding mechanisms of Hox gene activation through the identification of numerous enhancer elements which are located outside of the HoxA and HoxD clusters, within the large regulatory landscapes that flank the clusters. However, mechanisms for Hox gene silencing still remain largely elusive. Studies have demonstrated the important role for the Polycomb Group (PcG) protein complexes in the transcriptional repression of the Hox genes during development. Therefore, the aim of my thesis was to study the functional role of the PcG proteins in HoxA gene regulation during limb development. We first studied the functional role of the PcG proteins in organizing the chromatin architecture at and around the HoxA cluster. ChIP-seq experiments to map the binding of the Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2) in the proximal and distal limb bud at embryonic day 12.5 (E12.5) revealed that PcG occupancy correlated with the dynamic expression of the HoxA genes in the proximal and distal limb. Moreover, to study the functional link between PcG occupancy and chromatin organization we performed 5C (Chromosome Conformation Capture Carbon Copy), which allows for the detection of long-range spatial interactions between two genomic loci of interest. Our 5C analyses revealed that PcG bound loci physically interact in the 3D-environment, and that these contacts are lost upon PRC2 inactivation. In addition, we show that the differences in chromatin architecture which distinguish the proximal from distal limb were abrogated upon loss of PRC2 function. The resulting changes in chromatin architecture demonstrate that PRC2 is required to prevent certain enhancer-promoter interactions in the proximal limb in order to maintain Hoxa13 gene repression, whereas unexpectedly, we also find that PRC2 function is required to favor other enhancer-promoter contacts needed for HoxA gene activation by modulating the chromatin organization via PcG-mediated long-range contacts. Next, we assessed the genome-wide binding dynamics of PRC1 and PRC2 during limb development and demonstrated the requirement of PRC2 for transcriptional regulation. Our analyses revealed that PRC1 and PRC2 target genes involved in developmental processes and that the inactivation of PRC2 results in an up-regulation of these target genes. Strikingly, our analyses also reveal that PRC1 occupancy is unaffected by PRC2 inactivation, which reveals that a complex functional relationship between PRC1 and PRC2 exists during development. Finally, we show that while PRC2 inactivation does not globally affect proximal and distal limb identity, PRC2 is necessary to maintain the proper Hox transcriptional programs in the proximal and distal limb. Altogether this work emphasizes the important role of PcG proteins in regulating Hox gene expression during limb development. Importantly, we identified the contribution of PcG proteins in modulating the chromatin architecture at the HoxA cluster to promote gene activation and silencing. Moreover, we uncovered a dynamic relationship between PRC1 and PRC2 occupancy on a genome-wide scale, which correlates to transcriptional regulation during limb development. Overall, this work provides insights into the complex relationship between gene activation and repression during development processes"--

Download or read book Polycomb Group Proteins written by Vincenzo Pirrotta and published by Academic Press. This book was released on 2017-01-01 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: Polycomb Group Proteins is a comprehensive volume detailing the mechanisms that are key to the management of genome function in many different contexts, from embryonic stem cells to terminal differentiation. The book discusses the regulation of cell lineages, cell proliferation, apoptosis, X chromosome inactivation, and most major genome programming choices. In the last few years, the biochemical understanding of PRC1-type complexes has greatly expanded in terms of the number of components involved and the intricacies of their interactions. The functionalities of these various complexes and their components are not all well understood, but recent work has shown an important division of labor and roles in the recruitment of stable binding in the ability to lay the groundwork of histone modifications and in the epigenetic maintenance of repressed states. In an effort to provide clarity in this topical research area, the book provides a cluster of chapters that deal with variant PRC1 complexes, their taxonomy, their components, their interactions, and what is known of their functions. Provides topical coverage on accessory components that are known to be involved in PcG recruitment in Drosophila and their less understood role in mammals Includes dedicated sections on PRC1 complexes and PRC2 complexes for quick reference Features the role of RNA molecules in different aspects of Polycomb proteins involvement in epigenetic regulation, beginning with the key role of the Xist RNA in recruiting and spreading PcG complexes on the inactive X chromosome

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 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 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 Chromatin Signaling and Diseases written by Olivier Binda and published by Academic Press. This book was released on 2016-08-06 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chromatin Signaling and Diseases covers the molecular mechanisms that regulate gene expression, which govern everything from embryonic development, growth, and human pathologies associated with aging, such as cancer. This book helps researchers learn about or keep up with the quickly expanding field of chromatin signaling. After reading this book, clinicians will be more capable of explaining the mechanisms of gene expression regulation to their patients to reassure them about new drug developments that target chromatin signaling mechanisms. For example, several epigenetic drugs that act on chromatin signaling factors are in clinical trials or even approved for usage in cancer treatments, Alzheimer's, and Huntington's diseases. Other epigenetic drugs are in development to regulate various class of chromatin signaling factors. To keep up with this changing landscape, clinicians and doctors will need to stay familiar with genetic advances that translate to clinical practice, such as chromatin signaling. Although sequencing of the human genome was completed over a decade ago and its structure investigated for nearly half a century, molecular mechanisms that regulate gene expression remain largely misunderstood. An emerging concept called chromatin signaling proposes that small protein domains recognize chemical modifications on the genome scaffolding histone proteins, facilitating the nucleation of enzymatic complexes at specific loci that then open up or shut down the access to genetic information, thereby regulating gene expression. The addition and removal of chemical modifications on histones, as well as the proteins that specifically recognize these, is reviewed in Chromatin Signaling and Diseases. Finally, the impact of gene expression defects associated with malfunctioning chromatin signaling is also explored. Explains molecular mechanisms that regulate gene expression, which governs everything from embryonic development, growth, and human pathologies associated with aging Educates clinicians and researchers about chromatin signaling, a molecular mechanism that is changing our understanding of human pathology Explores the addition and removal of chemical modifications on histones, the proteins that specifically recognize these, and the impact of gene expression defects associated with malfunctioning chromatin signaling Helps researchers learn about the quickly expanding field of chromatin signaling

Download or read book HiC Pro an Optimized and Flexible Pipeline for Hi C Data Processing written by Oldenburg Oldenburg Press and published by . This book was released on 2016-01-29 with total page 40 pages. Available in PDF, EPUB and Kindle. Book excerpt: HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro.

Download or read book Handbook of Epigenetics written by Trygve O Tollefsbol and published by Academic Press. This book was released on 2017-07-10 with total page 684 pages. Available in PDF, EPUB and Kindle. Book excerpt: Handbook of Epigenetics: The New Molecular and Medical Genetics, Second Edition, provides a comprehensive analysis of epigenetics, from basic biology, to clinical application. Epigenetics is considered by many to be the new genetics in that many biological phenomena are controlled, not through gene mutations, but rather through reversible and heritable epigenetic processes. These epigenetic processes range from DNA methylation to prions. The biological processes impacted by epigenetics are vast and encompass effects in lower organisms and humans that include tissue and organ regeneration, X-chromosome inactivation, stem cell differentiation, genomic imprinting, and aging. The first edition of this important work received excellent reviews; the second edition continues its comprehensive coverage adding more current research and new topics based on customer and reader reviews, including new discoveries, approved therapeutics, and clinical trials. From molecular mechanisms and epigenetic technology, to discoveries in human disease and clinical epigenetics, the nature and applications of the science is presented for those with interests ranging from the fundamental basis of epigenetics, to therapeutic interventions for epigenetic-based disorders. Timely and comprehensive collection of fully up-to-date reviews on epigenetics that are organized into one volume and written by leading figures in the field Covers the latest advances in many different areas of epigenetics, ranging from basic aspects, to technologies, to clinical medicine Written at a verbal and technical level that can be understood by scientists and college students Updated to include new epigenetic discoveries, newly approved therapeutics, and clinical trials

Download or read book Epigenetics of Aging written by Trygve O. Tollefsbol and published by Springer Science & Business Media. This book was released on 2009-11-11 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent studies have indicated that epigenetic processes may play a major role in both cellular and organismal aging. These epigenetic processes include not only DNA methylation and histone modifications, but also extend to many other epigenetic mediators such as the polycomb group proteins, chromosomal position effects, and noncoding RNA. The topics of this book range from fundamental changes in DNA methylation in aging to the most recent research on intervention into epigenetic modifications to modulate the aging process. The major topics of epigenetics and aging covered in this book are: 1) DNA methylation and histone modifications in aging; 2) Other epigenetic processes and aging; 3) Impact of epigenetics on aging; 4) Epigenetics of age-related diseases; 5) Epigenetic interventions and aging: and 6) Future directions in epigenetic aging research. The most studied of epigenetic processes, DNA methylation, has been associated with cellular aging and aging of organisms for many years. It is now apparent that both global and gene-specific alterations occur not only in DNA methylation during aging, but also in several histone alterations. Many epigenetic alterations can have an impact on aging processes such as stem cell aging, control of telomerase, modifications of telomeres, and epigenetic drift can impact the aging process as evident in the recent studies of aging monozygotic twins. Numerous age-related diseases are affected by epigenetic mechanisms. For example, recent studies have shown that DNA methylation is altered in Alzheimer’s disease and autoimmunity. Other prevalent diseases that have been associated with age-related epigenetic changes include cancer and diabetes. Paternal age and epigenetic changes appear to have an effect on schizophrenia and epigenetic silencing has been associated with several of the progeroid syndromes of premature aging. Moreover, the impact of dietary or drug intervention into epigenetic processes as they affect normal aging or age-related diseases is becoming increasingly feasible.

Download or read book The Functional Nucleus written by David P. Bazett-Jones and published by Springer. This book was released on 2016-10-17 with total page 501 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book gives an in-depth overview on nuclear structure and function. It clearly shows that the epigenome and the three-dimensional organization of the nucleus are not independent properties. The intimate relationship between the location and the epigenetic modifications of gene loci is highlighted. Finally, it shows that the complex three-dimensional organization of the nucleus is not just of academic interest: The structure, composition and function of virtually all of the sub-nuclear compartments identified so far can be implicated to a list of human genetic diseases. Hence, a detailed elucidation of how these domains are assembled and function will provide new opportunities for therapeutic intervention in clinical practice.

Download or read book The Regulatory Genome written by Eric H. Davidson and published by Elsevier. This book was released on 2010-07-19 with total page 303 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. The author, Eric Davidson, has been instrumental in elucidating this relationship. He is a world renowned scientist and a major contributor to the field of developmental biology. The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. New insights into the mechanisms of body plan evolution are derived from considerations of the consequences of change in developmental gene regulatory networks. Examples of crucial evidence underscore each major concept. The clear writing style explains regulatory causality without requiring a sophisticated background in descriptive developmental biology. This unique text supersedes anything currently available in the market. The only book in the market that is solely devoted to the genomic regulatory code for animal development Written at a conceptual level, including many novel synthetic concepts that ultimately simplify understanding Presents a comprehensive treatment of molecular control elements that determine the function of genes Provides a comparative treatment of development, based on principles rather than description of developmental processes Considers the evolutionary processes in terms of the structural properties of gene regulatory networks Includes 42 full-color descriptive figures and diagrams

Download or read book Genes Signals written by Mark Ptashne and published by CSHL Press. This book was released on 2002 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: P. 103.

Download or read book Centromeres and Kinetochores written by Ben E. Black and published by Springer. This book was released on 2017-08-23 with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the latest advances concerning the regulation of chromosome segregation during cell division by means of centromeres and kinetochores. The authors cover both state-of-the-art techniques and a range of species and model systems, shedding new light on the molecular mechanisms controlling the transmission of genetic material between cell divisions and from parent to offspring. The chapters cover five major areas related to the current study of centromeres and kinetochores: 1) their genetic and epigenetic features, 2) key breakthroughs at the molecular, proteomic, imaging and biochemical level, 3) the constitutive centromere proteins, 4) the role of centromere proteins in the physical process of chromosome segregation and its careful orchestration through elaborate regulation, and 5) intersections with reproductive biology, human health and disease, as well as chromosome evolution. The book offers an informative and provocative guide for newcomers as well as those already acquainted with the field.

Download or read book Human Epigenomics written by Carsten Carlberg and published by Springer. This book was released on 2018-02-01 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt: The term epigenetics describes regulatory and information storing mechanisms of specific genes that do not involve any change of their DNA sequence. Epigenetics is closely related to the extensively folded state, in which the genome is packaged, known as chromatin. New genomic tools nowadays allow the genome-wide assessment of, for example, chromatin states and DNA modifications, and led to the discovery of unexpected new epigenetic principles, such as epigenomic memory. This was the start of the field of epigenomics, the relation of which to human health and disease is discussed in this textbook. This book aims to summarize, in a condensed form, the role of epigenomics in defining chromatin states that are representative of active genes (euchromatin) and repressed genes (heterochromatin). Moreover, this book discusses the principles of gene regulation, chromatin stability, genomic imprinting and the reversibility of DNA methylation and histone modifications. This information should enable a better understanding of cell type identities and will provide new directions for studies of, for example, cellular reprograming, the response of chromatin to environmental signals and epigenetic therapies that can improve or restore human health. In order to facilitate the latter, we favor a high figure-to-text ratio following the rule “a picture tells more than thousand words”. The content of the book is based on the lecture course “Molecular Medicine and Genetics” that is given by one of us (C. Carlberg) in different forms since 2002 at the University of Eastern Finland in Kuopio. Thematically, this book is located between our textbooks “Mechanisms of Gene Regulation” (ISBN 978-94-017-7741-4) and “Nutrigenomics” (ISBN 978-3-319-30415-1), studying of which may also be interesting to our readers. The book is sub-divided into three sections and 13 chapters. Following the Introduction (section A), section B will explain the molecular basis of epigenomics, while section C will provide examples for the impact of epigenomics in human health and disease. The lecture course is primarily designed for Master level students of biomedicine, but is also frequented by PhD students as well as by students of other bioscience disciplines. Besides its value as a textbook, Human Epigenomics will be a useful reference for individuals working in biomedicine.

Download or read book Gynaecological Malignancies written by Gwo Yaw Ho and published by BoD – Books on Demand. This book was released on 2020-06-17 with total page 130 pages. Available in PDF, EPUB and Kindle. Book excerpt: “Gynaecological Malignancies - Updates and Advances” aims to present a review of the significant advances in the understanding and management of gynaecological malignancies. Major areas of importance in this field will be covered, incorporating new knowledge that has arisen due to the advancements in molecular techniques and the ability to correlate these molecular changes with clinical behaviour of gynaecologic tumours. The therapeutic implications of molecular subtyping to match appropriate therapies and the appreciation of the use of up to date radiotherapy techniques will be explored.

Download or read book Cell and Tissue Interactions written by James W. Lash and published by . This book was released on 1977 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Epigenetic Cancer Therapy written by Steven Gray and published by Academic Press. This book was released on 2015-07-01 with total page 748 pages. Available in PDF, EPUB and Kindle. Book excerpt: Epigenetic Cancer Therapy unites issues central to a translational audience actively seeking to understand the topic. It is ideal for cancer specialists, including oncologists and clinicians, but also provides valuable information for researchers, academics, students, governments, and decision-makers in the healthcare sector. The text covers the basic background of the epigenome, aberrant epigenetics, and its potential as a target for cancer therapy, and includes individual chapters on the state of epigenome knowledge in specific cancers (including lung, breast, prostate, liver). The book encompasses both large-scale intergovernmental initiatives as well as recent findings across cancer stem cells, rational drug design, clinical trials, and chemopreventative strategies. As a whole, the work articulates and raises the profile of epigenetics as a therapeutic option in the future management of cancer. Concisely summarizes the therapeutic implications of recent, large-scale epigenome studies, including the cancer epigenome atlas Discusses targeted isoform specific versus pan-specific inhibitors, a rational drug design approach to epigenetics relevant to pharmacoepigenetic clinical applications Covers new findings in the interplay between cancer stem cells (CSCs) and drug resistance, demonstrating that epigenetic machinery is a candidate target for the eradication of these CSCs