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Author: Karim Mekhail
Publisher: Frontiers Media SA
ISBN: 288974504X
Category : Science
Languages : en
Pages : 139
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Book Description
Author: Karim Mekhail
Publisher: Frontiers Media SA
ISBN: 288974504X
Category : Science
Languages : en
Pages : 139
Get Book Here
Book Description
Author: Tom Sexton
Publisher: Springer Nature
ISBN: 1071624970
Category : Science
Languages : en
Pages : 332
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Book Description
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.
Author: Przemysław Szałaj (Doctor of Sciences: Statistics)
Publisher:
ISBN:
Category :
Languages : nl
Pages : 0
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Author: Przemyslaw Szalaj
Publisher:
ISBN:
Category :
Languages : en
Pages : 45
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Author: Narasimha Marella
Publisher:
ISBN:
Category :
Languages : en
Pages : 203
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Book Description
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.
Author: Max Garrett Kushner
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Gene expression is regulated by a number of different mechanisms, but of particular interest recently is the regulation of gene expression through spatial organization of the genome. Various techniques have been developed and continue to be developed to further characterize and study the dependence of transcriptional regulation on genome organization. In this dissertation, I will discuss a series of projects aimed at designing a novel method to examine the relationship between transcriptional activity and genomic contacts.I will discuss efforts to characterize photoactivatable compounds including members of the psoralen family for use as a tool to examine genomic contacts. I will explain the determination of many different photochemical properties of psoralen compounds. I will also mention optimization and the use of psoralen compounds with two-photon excitation. Here I present a technique we call Femto-Seq. This technique utilizes a photoactivatable DNA crosslinking compound with an affinity tag to take a snapshot of the DNA sequences spatially around a genomic locus of interest. After allowing the photoactivatable compound to intercalate, two-photon excitation is used to covalently bind sequences in a nuclear volume of interest (around a fluorescently labeled gene for example). The affinity tag on the crosslinker is used to enrich for sequences from the irradiated volume which are then analyzed through sequencing. I will present pilot experiments designed to examine the efficacy of such a method by looking at the enrichment of a targeted transgene. We report a 15-fold enrichment of the transgene matching expected enrichment based on the nuclear volume of interest. I will describe potential applications and extensions of such a technique. Many parts of the Femto-Seq method can be further optimized. Since the technique involves fluorescently labeling a genomic locus of interest, fluorescently labeled engineerable DNA binding proteins are particularly valuable. While many exist, we were particularly interested in Transcription Activator Like Effectors (TALEs). In order to understand the mechanisms of TALE binding we utilized a variety of techniques including DNA curtains, single molecule co-localization and Fluorescent Correlation Spectroscopy. I will also discuss the potential use of microfluidic platforms to increase throughput of the pulldown and cleanup processes.
Author: Aleksei Anatoliyovych Stepanenko
Publisher: Delve Publishing
ISBN: 9781773610290
Category :
Languages : en
Pages : 0
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Book Description
The human body consists of many trillions of cells harboring nearly identical genomes. Yet cells manifest strikingly different cell morphologies and functions, reflecting their distinct patterns of gene expression. One of the most fundamental questions in human biology is how one genome sequence can give rise to so many different cell types. Increasing evidence indicates that the spatial, three-dimensional (3D) organization of chromatin influences gene expression and cell fate. The spatial organization of metazoan genomes has a direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. Advancements in high-throughput genomics and computational methods in the past 15 years have taken our understanding of the genome to a whole new level by allowing genome-wide assessments of chromatin conformation in the 3D space. General principles guiding the spatial conformation of chromosomes, such as compartmentalization and formation of topologically associating domains and chromatin loops, are now becoming increasingly understood, and this is leading to a better understanding of long-range chromosomal communication. In this book, recent studies concerning the chromatin compaction, local interactions, long-range interactions and the nuclear positioning of each chromatin type are reviewed. The well-established and emerging technologies that are revolutionizing our understanding of higher-order genome architecture are summarized.
Author: Oldenburg Oldenburg Press
Publisher:
ISBN: 9781523764426
Category :
Languages : en
Pages : 40
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Book Description
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.
Author: Eric H. Davidson
Publisher: Elsevier
ISBN: 0080525598
Category : Science
Languages : en
Pages : 274
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Book Description
The interaction between biology and evolution has been the subject of great interest in recent years. Because evolution is such a highly debated topic, a biologically oriented discussion will appeal not only to scientists and biologists but also to the interested lay person. This topic will always be a subject of controversy and therefore any breaking information regarding it is of great interest.The author is a recognized expert in the field of developmental biology and has been instrumental in elucidating the relationship between biology and evolution. The study of evolution is of interest to many different kinds of people and Genomic Regulatory Systems: In Development and Evolution is written at a level that is very easy to read and understand even for the nonscientist. * Contents Include* Regulatory Hardwiring: A Brief Overview of the Genomic Control Apparatus and Its Causal Role in Development and Evolution * Inside the Cis-Regulatory Module: Control Logic and How the Regulatory Environment Is Transduced into Spatial Patterns of Gene Expression* Regulation of Direct Cell-Type Specification in Early Development* The Secret of the Bilaterians: Abstract Regulatory Design in Building Adult Body Parts* Changes That Make New Forms: Gene Regulatory Systems and the Evolution of Body Plans
Author: Andrew Colin Payne
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
We conclude with a discussion of IGS scaling properties, by which we can anticipate many-fold future improvements in yield and resolution. We anticipate IGS and related scalable in situ methods will be instrumental in unifying genomics and microscopy, enabling scientists to map genome organization from single base pairs to whole organisms and ultimately to connect genome structure and function.
