Download or read book Capturing Chromosome Conformation written by Beatrice Bodega and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Capturing Chromosome Conformation written by Beatrice Bodega and published by Humana. This book was released on 2020-10-29 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Approaches to Analysis of Chromosome Conformation Capture Data written by Joachim Wolff and published by . This book was released on 2022* with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Chromosome Conformation Capture on Chip 4C written by Marieke Johanna Simonis and published by . This book was released on 2008 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Chromatin Immunoprecipitation Assays written by Philippe Collas and published by Methods in Molecular Biology. This book was released on 2009-08-25 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Plant Chromatin Dynamics written by Marian Bemer and published by Humana. This book was released on 2018-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Hi C Data Analysis written by Silvio Bicciato and published by Humana. This book was released on 2022-09-04 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Patterns and Processes Driving Chromosome Organization written by Sameer Abraham (Physicist) and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Innate Antiviral Immunity written by Karen Mossman and published by . This book was released on 2017 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book HiC Pro an Optimized and Flexible Pipeline for Hi C Data Processing written by Oldenburg Oldenburg Press and published by . This book was released on 2016-01-29 with total page 40 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Technologies for Protein and RNA focused Chromosome Conformation written by Maxwell Robert Mumbach and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Plant Genomics written by Wolfgang Busch and published by Humana Press. This book was released on 2018-07-20 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides protocols that revolve around three pillars of progress in the plant genomics field: genotypes, phenotypes, and the molecular processes in between. Chapters in Plant Genomics: Methods and Protocols are not restricted to the predominant model species Arabidopsis thaliana, hoping to encourage and facilitate other researchers to expand their research to other species. 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 practical, Plant Genomics: Methods and Protocols aims to serve as an inspiration for further studies in plant genomics.
Download or read book Eukaryotic Transcriptional and Post Transcriptional Gene Expression Regulation written by Narendra Wajapeyee and published by . This book was released on 2016 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume describes a variety of protocols that will allow the readers to study different aspects of transcriptional and posttranscriptional gene expression regulation in eukaryotic cells. Chapters focus on the latest use of CRISPRi and RNAi technologies for studying various aspects of transcriptional and posttranscriptional regulation and tools to navigate protocols on key bioinformatics. 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, Eukaryotic Transcription and Post-Transcription Gene Expression Regulation aims to ensure successful results in the further study of this vital field.
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:
Download or read book Parasite Genomics written by Luis M. de Pablos and published by Humana. This book was released on 2021-07-28 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed book provides a comprehensive series of innovative research techniques and methodologies applied to the parasite genomics research area, all applying different approaches to analyzing parasite genomes and furthering the study of genetic complexity and the mechanisms of regulation. Beginning with chapters on novel sequencing and the bioinformatics pipeline, the volume continues by exploring diagnostic approaches using genomic tools, host-parasite interactions, as well as the genomics of parasite-derived extracellular vesicles. 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, Parasite Genomics: Methods and Protocols creates a detailed picture of genomic approaches for researchers seeking a better understanding of characterizing parasite nucleic acid content.
Download or read book Chromosome Architecture written by Mark C. Leake and published by Humana. This book was released on 2016-06-10 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details a valuable collection of protocols and reviews, such as emerging experimental and theoretical approaches. These approaches have resulted in a substantial improvement in the understanding of chromosome architecture. Chromosome Architecture: Methods and Protocols guides readers through cutting-edge interdisciplinary methods which allow for an understanding of architecture of chromosomes with exceptionally enhanced resolution, both in terms of space and time. 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, Chromosome Architecture: Methods and Protocols aims to ensure successful results in the further study of this vital field.
Download or read book Epigenetics and Systems Biology written by Leonie Ringrose and published by Academic Press. This book was released on 2017-04-25 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Epigenetics and Systems Biology highlights the need for collaboration between experiments and theoretical modeling that is required for successful application of systems biology in epigenetics studies. This book breaks down the obstacles which exist between systems biology and epigenetics researchers due to information barriers and segmented research, giving real-life examples of successful combinations of systems biology and epigenetics experiments. Each section covers one type of modeling and one set of epigenetic questions on which said models have been successfully applied. In addition, the book highlights how modeling and systems biology relate to studies of RNA, DNA, and genome instability, mechanisms of DNA damage signaling and repair, and the effect of the environment on genome stability. Presents original research in a wider perspective to reveal potential for synergies between the two fields of study Provides the latest experiments in primary literature for the modeling audience Includes chapters written by experts in systems biology and epigenetics who have vast experience studying clinical applications
