The Role Of High Order Chromatin Organization In Gene Regulation

Author : Alexey V. Pindyurin
Publisher : Frontiers Media SA
ISBN 13 : 2832505295
Total Pages : 248 pages
Book Rating : 4.98/5 ( download)

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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:

Author : Anita Göndör
Publisher : Academic Press
ISBN 13 : 0128034025
Total Pages : 496 pages
Book Rating : 4.26/5 ( download)

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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

Author : Sarah C. R. Elgin
Publisher : Frontiers in Molecular Biology
ISBN 13 : 9780199638901
Total Pages : 372 pages
Book Rating : 4.0X/5 ( download)

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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.

Author : Bruce Alberts
Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.81/5 ( download)

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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:

Author : Morgan Welsh Bernier
Publisher :
ISBN 13 :
Total Pages : 139 pages
Book Rating : 4.43/5 ( download)

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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.

Author : Esteban Ballestar
Publisher : Springer
ISBN 13 : 9781441982179
Total Pages : 182 pages
Book Rating : 4.75/5 ( download)

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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.

Author : Altuna Akalin
Publisher : CRC Press
ISBN 13 : 1498781861
Total Pages : 462 pages
Book Rating : 4.62/5 ( download)

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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.

Author : Paul Robert Munn
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.76/5 ( download)

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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.

Author : Roeland van Driel
Publisher : Oxford University Press, USA
ISBN 13 : 9780198549222
Total Pages : 295 pages
Book Rating : 4.29/5 ( download)

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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.

Author : Min Kim
Publisher :
ISBN 13 :
Total Pages : 99 pages
Book Rating : 4.93/5 ( download)

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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.