Spatial Genome Organization
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Spatial Genome Organization
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Author : Karim Mekhail
language : en
Publisher: Frontiers Media SA
Release Date : 2022-02-23
Spatial Genome Organization written by Karim Mekhail and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-02-23 with Science categories.
Spatial Genome Organization
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Author : Tom Sexton
language : en
Publisher: Springer Nature
Release Date : 2022-07-22
Spatial Genome Organization written by Tom Sexton and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-07-22 with Science categories.
This detailed volume explores a variety of cutting-edge techniques used to interrogate spatial genome organization. Beginning with a section covering the vital chromosome conformation capture (3C) technique, this collection continues with chapters on targeted Hi-C approaches, sequencing-based approaches to assess nuclear environment, as well as single-cell technologies to better characterize the heterogeneity and dynamics of nuclear architectures and approaches to visualize them by microscopy. Finally, in order to be able to ask functional questions about the role of spatial chromatin organization in genomic control, the last section provides methods for acute manipulations of chromatin architecture. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Spatial Genome Organization: Methods and Protocols is an ideal resource for researchers searching for the best techniques to address their own specific research questions.
Modeling And Analysis Of Spatial Genome Organization
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Author : Przemysław Szałaj (Doctor of Sciences: Statistics)
language : nl
Publisher:
Release Date : 2019
Modeling And Analysis Of Spatial Genome Organization written by Przemysław Szałaj (Doctor of Sciences: Statistics) and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019 with categories.
Spatial Genome Organization
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Author : Narasimha Marella
language : en
Publisher:
Release Date : 2009
Spatial Genome Organization written by Narasimha Marella and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009 with categories.
The mammalian genome is housed in a membrane bound organelle referred to as the nucleus. The three dimensional structural organization of the nucleus has been implicated to affect various genomic functions. Each chromosome in the interphase cell nuclei occupies a distinct region called the chromosome territory. Advances in cytogenetic techniques including fluorescence insitu hybridization and development of chromosome specific probes have allowed visualization of these individual territories within the interphase nuclei. The organization of the chromosome territories within the nuclear environment is highly debatable as it seems to be influenced by chromosome size or by gene density. Changes in the spatial organization of the chromosomes during differentiation and conservation of territorial associations within various tissue and cell types are also less understood aspects of genomic organization.^It is known that aberrations in the spatial and temporal organization of the genome leads to expression of disease phenotypes like cancer. However this phenomenon has been exemplified in only a few studies. In order to provide a deeper understanding of the above mentioned aspects of spatial genomic organization and its influence on gene regulation we have performed chromosome territory labeling experiments on a subset of six human chromosomes by adopting a RE-FISH (repeated fluorescence insitu hybridization) in a normal diploid human fibroblast (WI38) and a normal breast epithelial (MCF10A) cell line. We identified a tissue specific organization for these chromosomes within each of these cell lines by employing a novel computer graphing algorithm referred to as the generalized median graph (GMG). The radial positioning of the chromosomes showed a linear correlation with the chromosome size in both cell lines.^We were also able to measure the chromosome-chromosome associations for our subset of chromosomes using in house developed algorithms (Chapter 2). Our study on chromosome 18 and 19 organization during keratinocyte differentiation suggests significant stage specific shifts in chromosome territory spatial positions during differentiation (Chapter 3). We further extended our investigations on genome organization from chromosome territories to individual genes. FISH experiments were performed with individual cosmid probes as well as BAC probes to elucidate the organization of the human type I interferon gene cluster on metaphase chromosomes of the human osteosarcoma cell line (MG63) and normal diploid fibroblasts (Chapter 4). Both the cosmid and BAC probes consistently showed a six fold ladder-like genomic amplification of the interferon gene cluster on one chromosome in the MG63 cell line termed the `interferon chromosome'. This amplification was absent on WI38 metaphase chromosomes.^Comparative genomic hybridization (CGH) analysis also confirmed this gene amplification. We also found that centromere and whole chromosome regions of chromosomes 4 and 9 were interspersed with the amplified gene cluster on the interferon chromosome. Based on the results of our study, we propose a model involving the breakage- fusion -bridge theory for the generation of the interferon chromosome in the MG63 cell line (Chapter 4). Finally in this thesis, we investigate the relationship of alterations in spatial organization and genomic amplification to aberrant changes in gene expression in cancer. The MCF10A series of breast epithelial cell lines consisting of a normal MCF10A, premalignant MCF10At1 and malignant MCF10CA1a were utilized in these studies. Spectral Karyotyping (SKY) and CGH analyses were performed on all three cell lines. Two color gene expression analyses were carried out on mRNA isolated from normal MCF10A and malignant MCF10CA1a cell lines.^A total of 8000 genes were identified that showed at least two fold changes- either up or down regulated. Structural changes observed by CGH and SKY were correlated with the gene expression changes. Our results showed that a direct correlation between modifications in genomic structure and changes in gene expression does not exist in a majority of the observed genes (Chapter 5). Overall, the experiments done in this thesis highlight and explore the relationships between the spatial and temporal organization in the nucleus and its influence on genomic function.^The thesis is divided into the following six chapters:Chapter1: IntroductionChapter 2: Tissue specific chromosome organization in normal and cancer cell nuclei Chapter 3: Distinct changes in chromosome arrangements during human epidermal keratinocyte differentiation Chapter 4: Ladder-like amplification of the type I interferon gene cluster in the human osteosarcoma cell line MG63Chapter 5: Cytogenetic and functional analysis of breast cancer progression: Integration of spectral karyotyping, comparative genomic hybridization and cDNA microarray approachesChapter 6: Future Aims.
Nuclear Pore Complexes In Genome Organization Function And Maintenance
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Author : Maximiliano D’Angelo
language : en
Publisher: Springer
Release Date : 2018-02-02
Nuclear Pore Complexes In Genome Organization Function And Maintenance written by Maximiliano D’Angelo and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-02-02 with Medical categories.
The three-dimensional organization of the DNA inside the eukaryotic cell nucleus has emerged a critical regulator of genome integrity and function. Increasing evidence indicates that nuclear pore complexes (NPCs), the large protein channels that connect the nucleus to the cytoplasm, play a critical role in the establishment and maintenance of chromatin organization and in the regulation of gene activity. These findings, which oppose the traditional view of NPCs as channels with only one: the facilitation of nucleocytoplasmic molecule exchange, have completely transformed our understanding of these structures. This book describes our current knowledge of the role of NPCs in genome organization and gene expression regulation. It starts by providing an overview of the different compartments and structures of the nucleus and how they contribute to organizing the genome, then moves to examine the direct roles of NPCs and their components in gene expression regulation in different organisms, and ends by describing the function of nuclear pores in the infection and genome integration of HIV, in DNA repair and telomere maintenance, and in the regulation of chromosome segregation and mitosis. This book provides an intellectual backdrop for anyone interested in understanding how the gatekeepers of the nucleus contribute to safeguarding the integrity and function of the eukaryotic genome.
The Role Of High Order Chromatin Organization In Gene Regulation
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Author : Alexey V. Pindyurin
language : en
Publisher: Frontiers Media SA
Release Date : 2022-11-11
The Role Of High Order Chromatin Organization In Gene Regulation written by Alexey V. Pindyurin and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-11-11 with Science categories.
Self Organization In Biological Systems
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Author : Scott Camazine
language : en
Publisher: Princeton University Press
Release Date : 2003-09-17
Self Organization In Biological Systems written by Scott Camazine and has been published by Princeton University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003-09-17 with Art categories.
Biological structures built through mechanisms involving self-organization are examined in this text. Examples of such structures are termite mounds, which provide their inhabitants with a secure & stable environment. The text looks at why & how self-organization occurs in nature.
Modeling The 3d Conformation Of Genomes
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Author : Guido Tiana
language : en
Publisher: CRC Press
Release Date : 2019-01-15
Modeling The 3d Conformation Of Genomes written by Guido Tiana and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-01-15 with Science categories.
This book provides a timely summary of physical modeling approaches applied to biological datasets that describe conformational properties of chromosomes in the cell nucleus. Chapters explain how to convert raw experimental data into 3D conformations, and how to use models to better understand biophysical mechanisms that control chromosome conformation. The coverage ranges from introductory chapters to modeling aspects related to polymer physics, and data-driven models for genomic domains, the entire human genome, epigenome folding, chromosome structure and dynamics, and predicting 3D genome structure.
The Functional Nucleus
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Author : David P. Bazett-Jones
language : en
Publisher: Springer
Release Date : 2016-10-17
The Functional Nucleus written by David P. Bazett-Jones and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-10-17 with Science categories.
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.
Journal Of The National Cancer Institute
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Author :
language : en
Publisher:
Release Date : 1990
Journal Of The National Cancer Institute written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1990 with AIDS (Disease) categories.