Download or read book The Role of High Order Chromatin Organization in Gene Regulation written by Alexey V. Pindyurin and published by Frontiers Media SA. This book was released on 2022-11-11 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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 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 The Structure of Chromatin and Its Influence on Gene Regulation written by Morgan Welsh Bernier and published by . This book was released on 2014 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt: Eukaryotic DNA is organized into a structural polymer called chromatin which ultimately controls important DNA processing functions such as transcription, DNA repair and DNA replication. The fundamental unit of chromatin is the nucleosome which is made up of about 146 base pairs wrapped around a histone core. The histone core contains 2 copies each of the histones H2A, H2B, H3 and H4. Long strings of nucleosomes compact into higher order structures which are not well known, but play a pivotal role in DNA accessibility. There are many factors that affect higher order structure and compaction of chromatin including inter and intra nucleosome interactions, incorporation of linker histones (H1), and post translational modifications. This dissertation includes a detailed study of some of these mechanisms. The first study looks at the H3 N-terminal tail which is long, unstructured and heavily modified in vivo . Using Electron Paramagnetic Resonance and site directed spin labeling; we were able to observe the dynamics of the H3 tail within compacted 17-mer nucleosome arrays. We find that these tails maintain their mobility as the arrays compact and self-associate despite previous studies that suggested these tails make inter- and intra-nucleosome contacts during compaction. We conclude that these contacts are transient and permit the tails to maintain mobility and accessibility.

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 Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Computational Genomics with R written by Altuna Akalin and published by CRC Press. This book was released on 2020-12-16 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Download or read book Computational Approaches to Understanding Transcription Regulation written by Paul Robert Munn and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription regulation refers to the coordination of numerous processes and protein complexes that results in the production of RNA from DNA. Disruption of the process of transcription has been implicated in disease and developmental disorders, but despite intense study, aspects of transcription regulation continue to remain elusive. Work described here attempts to provide computational approaches with which to further our understanding these events. Studies in Chapter Two investigate the relationship between chromatin structure and transcription regulation. To fully understand gene regulation, we need to understand the processes driving higher order chromatin organization. The high level, territorial structure of interphase chromatin is well established, as are the building blocks of chromatin, the nucleosomes, that form the 10 nm fibers. However, the chromatin folding process that gets us from this basic, 10 nm fiber to the high-level territories is less well understood. I investigate whether changes in chromatin organization are a factor in the response of a cell to stress. To study this, the cell was perturbed via heat-shock and the change in expression measured for selected genes known to respond to heat-shock. Chromatin conformation was then measured, using the Hi-C assay, before and after heat-shock, focusing on the interactions between the enhancers and promoters of these selected genes. Changes in structure that either increase or decrease interactions between specific regions of chromatin after stress was applied would be evidence for these changes driving gene expression. In Chapter Three, I explore machine learning approaches to more fully exploit available precision nuclear run-on and sequencing (PRO-seq) data to improve genome annotations. The start and extent of transcription is very specific. By sequencing RNA transcripts, or by measuring factors that correlate with transcription (such as modifications to histones, or regions in which chromatin is accessible) we can infer the position of elements such as enhancers or promoters. I hypothesized that PRO-seq signal contains subtle patterns that have not been leveraged extensively by previous methods. Here I use two different neural network architectures to see whether inferring patterns in the signal gives my methods an advantage.

Download or read book Nuclear Organization Chromatin Structure and Gene Expression written by Roeland van Driel and published by Oxford University Press, USA. This book was released on 1997 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is one of the first books that focuses on emerging concepts about the role of the structure of chromatin, the organization of the genome, and the structure of the interphase nucleus in the control of gene expression in eukaryotes. The first section analyses the relationship between the dynamic chromatin structure at the nucleosome level and gene expression. Section two looks into higher order chromatin structure in relation to transcription. In section three the molecular basis ofepigenetic phenomena, like X-chromosome inactivation is discussed, starting from our understanding of chromatin structure. Together, these topics form the molecular basis for our understanding of cell differentiation, knowledge that is essential for the design of transgenic animals and plants and for gene therapy in humans. The book is of direct interest to students that are new in the field and to investigators in the area of biomolecular sciences, like developmental biology, biochemistry, cell biology, microbiology and genetics. Also, those working in applied fields of research, i.e biotechnology and biomedicine, will strongly benefit from this book. It will help them to understand fundamental problems in transgenics and gene therapy. Importantly, a variety of human disorders may turn out to be caused by genetic or somatic errors related to this level of gene control.

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 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 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 The Nucleus Second Edition written by Ana Pombo and published by . This book was released on 2021-09 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

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 Proteogenomics written by Ákos Végvári and published by Springer. This book was released on 2016-09-29 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book highlights key technologies and identifies areas for further development in proteogenomics. The utility and usefulness of very large Omics data sets (Next Gen Sequencing of DNA, RNA-seq, ribosome profiling, mass spectrometry- and antibody-based proteomics) is discussed and opportunities and challenges of related bioinformatics applications are outlined. The reader will be able to appreciate the interdisciplinary nature of the continuously evolving area of proteogenomics, which has already grown beyond its original concept of verifying gene annotations by proteomics. The chapters presented in this book are arranged to offer a general overview, rather than to provide detailed descriptions of technologies. The selected applications will provide useful insight into the level of detail that can be obtained in relation to certain diseases areas, including cancer biology and personalized medicine. The readers will find that each chapter delivers a comprehensive approach to proteogenomics, each from the point of view of a specific application. Research scientists interested in innovative processes that can offer a unique and at the same time a more complete access to technological developments and concepts that in turn can contribute to a better understand biological functions should read this book.

Download or read book Long Range Control of Gene Expression written by Veronica van Heyningen and published by Academic Press. This book was released on 2011-09-02 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: Long-Range Control of Gene Expression covers the current progress in understanding the mechanisms for genomic control of gene expression, which has grown considerably in the last few years as insight into genome organization and chromatin regulation has advanced. Discusses the evolution of cis-regulatory sequences in drosophila Includes information on genomic imprinting and imprinting defects in humans Includes a chapter on epigenetic gene regulation in cancer

Download or read book Bridging Chromatin Architecture to Gene Expression written by Jennifer Crutchley and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "There has been a great influx of information regarding the structures that our genome is packaged into, but how this occurs and how it relates to gene expression remains a mystery. Recently, Hi-C technology has revealed that our genome is organized in topological associated domains (TADs) and that at the boundaries of these TADs there is an increase of the previously characterized chromatin organization mediators, CTCF and cohesin. It is my objective to identify the role of CTCF and cohesin in the regulation of the gene expression and TAD boundary maintenance of the HOXA cluster. By employing siRNA and shRNA methodology in combination of 5C-seq technology, I identified that cohesin is the key mediator involved in maintaining the TAD boundary within the HOXA locus. Furthermore, loss of the cohesin complex resulted in an up-regulation of the 5'end HOXA genes, suggesting that the maintenance boundary is required to shut down the expression of the genes within that region. The results suggest that cohesin is the key mediator involved in the regulation and higher order chromatin structure of the HOXA cluster." --