Capturing Chromosome Conformation PDF Download
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Author: Beatrice Bodega
Publisher:
ISBN: 9781071606650
Category : Biology
Languages : en
Pages :
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Book Description
Author: Beatrice Bodega
Publisher:
ISBN: 9781071606650
Category : Biology
Languages : en
Pages :
Get Book Here
Book Description
Author: Beatrice Bodega
Publisher: Humana
ISBN: 9781071606636
Category : Science
Languages : en
Pages : 322
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Book Description
This detailed book collects methods based on the evolution of the chromosome conformation capture (3C) technique and other complementary approaches to dissect chromatin conformation with an emphasis on dissection of nuclear compartmentalization and visualization in imaging. 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, Capturing Chromosome Conformation: Methods and Protocols serves as an ideal guide for researchers working to further understand 3D genome organization.
Author: Joachim Wolff
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Author: Marieke Johanna Simonis
Publisher:
ISBN: 9789071382772
Category :
Languages : en
Pages : 171
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Book Description
Author: Philippe Collas
Publisher: Methods in Molecular Biology
ISBN:
Category : Computers
Languages : en
Pages : 290
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Book Description
In this book, researchers deeply involved in the development and improvement of chromatin immunoprecipitation assays (ChIP) provide cutting-edge protocols devoted to the most recent progress in ChIP and related subjects.
Author: Marian Bemer
Publisher: Humana
ISBN: 9781493984510
Category : Science
Languages : en
Pages : 0
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Book Description
This volume provides a comprehensive collection of protocols that can be used to study plant chromatin structure and composition. Chapters divided into three sections detail the profiling of chromatin features in relation to epigenetic regulation, investigate the interaction between chromatin modifications and gene regulation, and explore the 3D spatial organization of the chromatin inside the nucleus. Written in the highly successful Methods in Molecular Biology series format, 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 cutting-edge, Plant Chromatin Dynamics: Methods and Protocols aims to ensure successful results in the further study of this vital field.
Author: Sameer Abraham (Physicist)
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
In this thesis, we focus on different approaches to studying the organization of chromosomes with in the nucleus of cells. We employ both genomic analysis of chromosome interaction maps, and polymer simulations to answer various questions that are relevant to the field. The first two chapters of this thesis are centered around genomic analysis of interaction maps generated from Chromosome Conformation Capture (3C) technologies. We begin by analyzing data generated using a novel Micro-C protocol and assess its performance in comparison to established Hi-C. New computation tools are developed to extract, quantify and compare patterns detected in both techniques. We find that Micro-C can accurately recapitulate the patterns of interactions found in Hi-C. In addition, evidence for nucleosome scale structure is also detected in the data. Following this, the scope of the meta-analysis is expanded. We compared over 70 different human Hi-C and Micro-C libraries that vary in the biochemical parameters used in data generation. We extract trends that relate the protocol parameters to the observed patterns of enrichment found in the data. We find that libraries generated with a high degree of fragmentation are better at capturing fine scale organization, while those with larger fragments excel in capturing larger patterns and structures. In the final chapter, we explore the dynamic changes in chromosome organization through the early stages of cell division. We analyze experimental Hi-C of DT-40 chicken cells and uncover the role of Condensin in disassembling interphase chromatin structure during prophase. We develop a model for prophase condensation and explore different interactions between loop extruding Cohesins and Condensins. We find that non-trivial interactions between these complexes are required to accurately capture the dynamics of the data. Our findings extend the model of loop extrusion and highlight the role of interactions between SMC complexes in organizing chromosomes.
Author: Silvio Bicciato
Publisher: Humana
ISBN: 9781071613924
Category : Science
Languages : en
Pages : 0
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Book Description
This volume details a comprehensive set of methods and tools for Hi-C data processing, analysis, and interpretation. Chapters cover applications of Hi-C to address a variety of biological problems, with a specific focus on state-of-the-art computational procedures adopted for the data analysis. Written in the highly successful Methods in Molecular Biology series format, 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 cutting-edge, Hi-C Data Analysis: Methods and Protocols aims to help computational and molecular biologists working in the field of chromatin 3D architecture and transcription regulation.
Author: Karen Mossman
Publisher:
ISBN: 9781493972371
Category : Biomedicine
Languages : en
Pages : 275
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Book Description
This book explores methods to study the complex and evolving interplay between a virus and its host that range from model systems to the detection of chemical molecules. The collection starts with the application of humanized mice and zebrafish as model organisms to study virus-host interactions and induction of innate immune responses. Subsequent chapters outline diverse methods to detect small interfering RNAs, microRNAs, and virus-derived dsRNA from a variety of cells, tissues, and organisms, as well as to interrogating the cytosolic RNA and DNA sensing pathways, including using RNA PAMPs as molecular tools, purification of cGAMP from virus particles and infected cells, and mechanisms to visualize the subcellular localization and activation of the adaptor proteins MAVS and STING. Cutting-edge methods, including high-throughput and genome-wide CRISPR/Cas9 screens, chromosome conformation capture, and whole-exome sequencing, are described to identify novel mediators, pathways, and variants underlying host susceptibility. Given the importance of studying these pathways and players under physiologic conditions, methods describing the isolation of primary mouse sensory neurons and group 2 innate lymphoid cells are also provided. Finally, this collection comes full circle back to the whole organism level and concludes with epidemiological methods to investigate virus-host interactions and the induction of innate immunity. Written for the 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, Innate Antiviral Immunity: Methods and Protocols spans a diverse array of approaches to study and elucidate the intricacies of this vital area of study.
Author: Maxwell Robert Mumbach
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
If you unpack all of the DNA in a single cell and lay it out flat, it's about six feet long -- and yet it can all fit into a micron-scale nucleus. Not only does it fit, but it's folded within the nucleus precisely to allow for the same DNA sequence across cell types to be specifically accessed for distinct functions. My thesis sought to investigate how DNA is folded within a cell, and how this folding impacts gene regulation and human disease. There are currently two main approaches to measure DNA folding: imaging and chromosome conformation capture (3C) methods. Although imaging is incredibly powerful, it is limited in throughput and resolution. 3C relies on a proximity ligation -- generating a hybrid "contact" fragment of two pieces of DNA that are near each other in 3D space. While there are many 3C-based methods, arguably the most transformative is Hi-C, which applies next-generation sequencing to a 3C library and has identified multiple DNA organizational features within a cell. However, Hi-C is inherently restricted due to sampling space: all possible 3D interactions are being measured. Because of this, billions of sequencing reads are needed to start observing confident DNA interactions over background. To combat this sampling space issue, we developed a method called HiChIP, which combines chromatin immunoprecipitation (ChIP) with Hi-C, allowing for a directed view of long-range contacts associated with a protein factor of interest. HiChIP improves the yield of contact reads by over 10-fold and lowers the input requirement over 100-fold relative to that of previous methods. As a proof of principle, we performed HiChIP on cohesin, a protein complex that has been reported to stabilize chromatin loops. Cohesin HiChIP identified a similar set of loops as Hi-C maps with increased signal-to-background and ten-fold less sequencing. The HiChIP technology we developed allowed, for the first time, DNA folding to be measured in disease-relevant patient samples. Precisely measuring how the immune system operates is central to our understanding of autoimmune disease and cancer. However, due to technological limitations the principles that govern regulatory 3D interactions in disease-relevant patient samples have been incompletely understood. This gap in understanding is particularly problematic for interpreting the molecular functions of inherited risk factors for common human diseases, which reside in intergenic enhancers or other non-coding DNA features in up to 90% of cases. We therefore performed HiChIP on the enhancer and promoter-associated histone mark H3K27ac in sorted T cell subsets and examined DNA interactions to map autoimmune disease variants present in non-coding regions and identify which genes they contact with. We found that the majority of disease-associated enhancers interact with genes beyond the nearest gene in the linear genome, leading to a four-fold increase of potential target genes for these autoimmune disease SNPs. While protein-factors are well-known to regulate the 3D structure of the genome, less is known regarding RNA. However, specific RNAs, such as XIST and HOTTIP, have been reported to utilize the topology of the genome in order to carry out their functions. We therefore sought to modify the HiChIP method to enrich for DNA interactions focused around an RNA of interest (HiChIRP). Interestingly, we identified many RNAs that engage in different types of 3D interactions. For example, we found that the RNA lncRNA-EPS binds to the boundaries of topological domains, a layer of DNA organization, to then engage in 3D interactions and regulate target genes contained within the domain. In summary, my thesis provided an unprecedented view of the 3D genome through the development of novel genomic tools for the research community. Importantly, these tools enable 3D measurements: (1) efficiently with less sequencing needed, (2) in disease-relevant systems that could not be assayed previously, and (3) focused on regulatory RNAs, whose roles in DNA structure are incompletely understood. I have then applied these tools across many collaborations to better understand the roles of DNA folding in gene regulation and disease.
