The Role of High-Order Chromatin Organization in Gene Regulation
Author: Alexey V. Pindyurin
Publisher: Frontiers Media SA
Published: 2022-11-11
Total Pages: 248
ISBN-13: 2832505295
DOWNLOAD EBOOK →Author: Alexey V. Pindyurin
Publisher: Frontiers Media SA
Published: 2022-11-11
Total Pages: 248
ISBN-13: 2832505295
DOWNLOAD EBOOK →Author: Sarah C. R. Elgin
Publisher: Frontiers in Molecular Biology
Published: 2000
Total Pages: 372
ISBN-13: 9780199638901
DOWNLOAD EBOOK →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: K. Nagata
Publisher: Springer Science & Business Media
Published: 2007-12-03
Total Pages: 285
ISBN-13: 4431301305
DOWNLOAD EBOOK →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.
Author: Morgan Welsh Bernier
Publisher:
Published: 2014
Total Pages: 139
ISBN-13:
DOWNLOAD EBOOK →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: Bruce Alberts
Publisher:
Published: 2002
Total Pages: 0
ISBN-13: 9780815332183
DOWNLOAD EBOOK →Author: Min Kim
Publisher:
Published: 2013
Total Pages: 99
ISBN-13:
DOWNLOAD EBOOK →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.
Author: Anita Göndör
Publisher: Academic Press
Published: 2016-10-25
Total Pages: 496
ISBN-13: 0128034025
DOWNLOAD EBOOK →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: Altuna Akalin
Publisher: CRC Press
Published: 2020-12-16
Total Pages: 462
ISBN-13: 1498781861
DOWNLOAD EBOOK →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.