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New Insights Into 3d Chromatin Organization And Function
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Book Synopsis New Insights Into 3D Chromatin Organization and Function by : Lina Zheng
Download or read book New Insights Into 3D Chromatin Organization and Function written by Lina Zheng and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Precise and delicate 3D genome organization is fundamental to cellular homeostasis. Big data generated by high-throughput technologies has granted great opportunities to deepen our understanding of chromatin organization and function, particularly for non-coding DNA sequences which have long been considered "junk DNAs". This dissertation aims at illuminating the structural importance of the non-coding DNA sequences and elucidating the modular organization of the 3D genome from histone modifications. First, I performed network analysis on Hi-C 3D contact data to identify non-coding DNA regions forming many spatial contacts with other regions ("hubs") without epigenetic signals that could maintain the global 3D chromatin structure. Furthermore, I employed a small-world network on epigenetic histone modification data to identify a group of active enhancers and promoters harboring many 3D contacts ("hotspots") which can maintain broad 3D chromatin organization beyond enhancer-promoter interactions. Deletion of hubs and hotspots can produce a profound impact on 3D chromatin organization and cell viability. In addition, through investigation of the histone modification across cell types, I identified the regulation associated modules ("RAMs") that can not only reflect the modular organization of the 3D genome but also be better aligned with the chromatin function. These studies provide new insights into 3D genome organization and function, navigating future efforts in the mechanistic investigation of the 3D genome.
Book Synopsis Chromatin Architecture by : Kirti Prakash
Download or read book Chromatin Architecture written by Kirti Prakash and published by Springer. This book was released on 2017-02-20 with total page 199 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book sheds new light on the current state of knowledge concerning chromatin organization. Particular emphasis is given to the new imaging potential offered by super-resolution microscopy, which allows DNA imaging with a very high labeling density. From the early work on chromosomes by Walther Flemming in the nineteenth century to recent advances in genomics, the history of chromatin research now spans more than a century. The various milestones, such as the discovery of the double helix structure, the sequencing of the human genome, and the recent description of the genome in 3D space, show that understanding chromatin and chromosome function requires a clear understanding of its structure. Presenting cutting-edge data from super-resolution single molecule microscopy, the book demonstrates that chromatin manifests several levels of folding, from nucleosomes to chromosomes. Chromatin domains emerge as a new fundamental building block of chromatin architecture, with functions possibly related to gene regulation. A detailed description of chromatin folding in the pachytene stage of meiosis serves as a model for exploring this functionality, showing the apparent interplay between structure, function, and epigenetic regulation. Lastly, the book discusses possible new avenues of innovation to describe chromatin’s organization and functions. Gathering essential insights on chromatin architecture, the book offers students an introduction to microscopy and its application to chromatin organization, while also providing advanced readers with new ideas for future research.
Book Synopsis Plant Chromatin Dynamics by : Marian Bemer
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.
Book Synopsis Chromatin Structure and Gene Expression by : Sarah C. R. Elgin
Download or read book Chromatin Structure and Gene Expression written by Sarah C. R. Elgin and published by Frontiers in Molecular Biology. This book was released on 2000 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Understanding Gene Regulation at a Fine-scale by : Lin An
Download or read book Understanding Gene Regulation at a Fine-scale written by Lin An and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Mammalian genomes are spatially organized into different levels. The three-dimensional genome organization is essential for gene expression, as it reflects or possibly enables the physical interactions between distal regulatory elements and their target genes. The advances in chromatin conformation capture technologies in the past decade, have both expanded and refined our understanding of the multiple levels of chromatin organization. Among the current technologies, Hi-C technology shows the highest potential with its unbiased genome-wide coverage. It provides exceptional resources as well as challenges in understanding chromatin interactions in detail.Observations from Hi-C suggest that the chromatin forms frequent local interactions in specific regions, which are called as Topologically Associating Domains (TADs). While TADs are often interpreted as the structural units to study regulatory mechanism, previous observation shows that hierarchy is present in TADs, with smaller TADs nested within larger ones. Though several different TAD calling algorithms have been developed, limited research has been done to reliably identify hierarchical TAD structures and understand their roles in gene regulation. The first tool introduced in this thesis is an optimized nested TAD calling method (OnTAD), which can identify different levels of TADs in a biologically meaningful manner. By incorporating epigenetics and transcriptional information, our analyses bring new insights towards understanding the complex system of gene regulation.Investigations on site-to-site interactions (e.g. enhancer-gene pairs) from Hi-C data are often limited by their resolution. As Hi-C measures pair-wise interactions, improving resolution requires quadratic increasing of sequencing depth. Inspired by the super-resolution image technique, the second tool in this thesis is a deep convolutional neural network (HiCPlus) to impute the high-resolution Hi-C results from low-sequence depth Hi-C data. It shows the power to recover biologically and statistically significant chromatin interactions with improved resolution. We also applied HiCPlus to 20 different tissue/cell-types, which only have low-resolution experimental data, to provide the community with a useful resource to investigate chromatin interaction at a fine scale.Besides improving resolution on existing Hi-C data, the third tool in this thesis utilizes one-dimensional epigenetic features to predict three-dimensional chromatin interactions in Hi-C. It can provide support for studies in cell-types with no experimental Hi-C data available. Meanwhile, it also sheds light on understanding driving factors for chromatin interaction formation.In the last part of the thesis, I included our effort on generating comprehensive chromatin segmentation maps for cell populations in the mouse hematopoietic lineage. During this process, we observed an unexpected chromatin state that is enriched with high signal in most of the input features, termed as heterogeneous state. I presented our exploration in finding the cause of such state and solution to improve the final segmentation map.
Book Synopsis Introduction to Epigenetics by : Renato Paro
Download or read book Introduction to Epigenetics written by Renato Paro and published by Springer Nature. This book was released on 2021-03-23 with total page 215 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access textbook leads the reader from basic concepts of chromatin structure and function and RNA mechanisms to the understanding of epigenetics, imprinting, regeneration and reprogramming. The textbook treats epigenetic phenomena in animals, as well as plants. Written by four internationally known experts and senior lecturers in this field, it provides a valuable tool for Master- and PhD- students who need to comprehend the principles of epigenetics, or wish to gain a deeper knowledge in this field. After reading this book, the student will: Have an understanding of the basic toolbox of epigenetic regulation Know how genetic and epigenetic information layers are interconnected Be able to explain complex epigenetic phenomena by understanding the structures and principles of the underlying molecular mechanisms Understand how misregulated epigenetic mechanisms can lead to disease
Book Synopsis Investigation of 3D Chromatin Modularity in Mouse Development by : Xiaofu Wei
Download or read book Investigation of 3D Chromatin Modularity in Mouse Development written by Xiaofu Wei and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chromatin structure plays a crucial role in various genomic processes in eukaryotic cells, including genome replication, transcriptional silencing, and gene regulation. Extensive studies have focused on the three-dimensional organization of the genome, revealing the presence of topologically associating domains (TADs) and compartments, which are defined by spatial contacts identified through techniques such as Hi-C. However, understanding the direct role of histone modification in shaping the three-dimensional genome structure remains an ongoing challenge.This thesis investigates changing patterns of regulation-associated modules (RAMs) in mouse development to understand the organization and function of RAMs and their boundaries. RAMs, proposed in previous studies using human samples, offer insights into genome organization and regulation. However, comprehensive explanations for RAM formation, functions, and boundary factors are lacking. Using the "findRAM" tool, we have identified RAM regions and boundaries from a dataset of 72 mouse embryonic samples. Pairwise comparisons between tissues at specific time points and between subsequent times within the same tissue have revealed changes in RAMs. Through genome enrichment analysis of these regions, we have identified functional pathways, including cation binding, metal ion binding, and transcription-related pathways. Additionally, consensus RAM (cRAM) regions have been determined for each time point and tissue, highlighting regions that exhibit consistent patterns of RAMs and boundaries. Gene enrichment analysis has provided further support for some of the findings from pairwise comparisons, and these findings align with the potential mechanism of RAM boundary formation proposed in previous research on RAMs. In conclusion, this thesis investigates 3D chromatin modularity through RAM analysis in mouse development data. We have identified pathways and genes potentially involved in RAM boundary formation through computational prediction and discussed improvements for the RAM identification model. These findings contribute to our understanding of the formation and functions of RAMs and boundaries, which are determined by histone modification marks. Ultimately, these findings highlight the connection between the structural and functional modularity of the 3D genome.
Download or read book The Nucleus written by Ronald Hancock and published by Humana Press. This book was released on 2008-08-28 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although our understanding of the structure and activities of the cell nucleus and of the nanomachines which it contains is increasing rapidly, much remains to be learned. The application and continuing development of the new, powerful biochemical and biophysical methodologies described here are essential in this quest. In The Nucleus, researchers from more than forty leading international laboratories describe state-of-the-art methods for isolating nuclei and their components and for studying their structure and activities, including some pathology-associated features. Volume I: Nuclei and Subnuclear Structures presents an overview of features of the intranuclear environment, followed by the most recent procedures for isolating nuclei from a wide range of cell types including muscle cells, yeast, oocytes, cells with polytene nuclei, Arabidopsis, trypanosomes, and dinoflagellates. The latest methods are described for isolating and working with nucleoli, constitutive heterochromatin, pathology-associated inclusions, and chromatin and for examining glycosylation, sumoylation, and ADP-ribosylation of nuclear proteins. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain lists of necessary materials and reagents, readily reproducible protocols, and tips for troubleshooting and avoiding known pitfalls. The Nucleus, Volume I: Nuclei and Subnuclear Structures is an essential reference for scientists who are working on our rapidly growing understanding of the cell nucleus and its activities.
Book Synopsis Modeling the 3D Conformation of Genomes by : G. Tiana
Download or read book Modeling the 3D Conformation of Genomes written by G. Tiana and published by CRC Press. This book was released on 2021-03-31 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a timely summary of physical modeling approaches applied to biological datasets that describe conformational properties of chromosomes in the cell nucleus. The coverage ranges from introductory chapters to modeling aspects related to polymer physics, and data-driven models for genomic domains, and predicting 3D genome structur
Book Synopsis Long Non-coding RNA, Chromatin Structure and 3D Chromatin Organization by : Xue Qing Wang
Download or read book Long Non-coding RNA, Chromatin Structure and 3D Chromatin Organization written by Xue Qing Wang and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "The mammalian HOX genes encode highly-conserved transcription factors that have crucial roles in a variety of biological processes, including the establishment of the body plan during embryogenesis and limb formation in early development. Organized into four clusters named HOXA through D, these genes are expressed in a spatial and temporal manner, which can be induced by retinoic acid (RA). This distinct pattern of gene expression is regulated by several different elements including distant enhancers, dynamic changes in chromatin structure and organization, and by recently identified long non-coding RNAs (lncRNAs). Located at the 3' end of the HOXA gene cluster, the lncRNA HOTAIRM1 was first proposed to function as a transcriptional activator of proximal HOXA genes in NB4 promyelocytic leukemia cells. To gain insight into the regulatory mechanism of HOTAIRM1, we investigated its function in NT2-D1 embryonic carcinoma and NB4 cell lines. In NT2-D1 cells, HOTAIRM1 functions as a transcriptional repressor of the central HOXA genes during RA induction. We found that this repressive effect was mediated by changes in chromatin organization at the 3' end of the cluster and alterations to the chromatin landscape through HOTAIRM1's interactions with both polycomb repressive complex 2 (PRC2) and UTX demethylase. From these results, we proposed that HOTAIRM1 potentiates the collinear activation of HOXA genes in NT2-D1 by effecting changes to both chromatin organization and structure. In contrast to this repressive function in NT2-D1 cells, we observed that HOTAIRM1's role as a transcriptional activator of proximal HOXA genes in NB4 cells was due to the drastically different histone landscape present within the gene cluster. As our work with HOTAIRM1 suggested that local chromatin structure can strongly influence the regulatory function of a lncRNA, we devised a new methodology termed Carbon-Copy Chromatin Immunoprecipitation (2C-ChIP) to evaluate the incremental changes in histone modifications and chromatin-bound proteins at the HOXA locus during RA induction of NT2-D1 cells. We observed that the activation of the 3' genes was primarily driven by the loss of both H3K27me3 and the PRC2 subunit SUZ12 up to a distinct boundary, bound by CTCF, located between the HOXA6 and HOXA7 genes. Chromosome conformation capture carbon copy (5C) analysis demonstrated significant rearrangement in chromatin organization at the proximal region of the cluster accompanying the changes to chromatin structure. The collection of work found within this thesis demonstrates how the cell-type specific regulatory function of HOTAIRM1 is derived from the local chromatin environment at the HOXA locus. Furthermore, the induction of the HOXA genes is driven by simultaneous changes to chromatin structure and 3D chromatin organization." --
Book Synopsis Chromatin and Disease by : Tapas K. Kundu
Download or read book Chromatin and Disease written by Tapas K. Kundu and published by Springer. This book was released on 2010-11-11 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book includes a collection of articles with the broad theme of disease connection to chromatin structure and function. It elaborates on the molecular pharmacology of the drugs targeting chromatin structure and its components. The book contains up-to-date information about the chromatin structure and chromatin related diseases and drug functions. This work is the first endeavor to present different aspects encompassing the above theme.
Book Synopsis Chromatin Protocols by : Srikumar P. Chellappan
Download or read book Chromatin Protocols written by Srikumar P. Chellappan and published by Humana Press. This book was released on 2010-07-09 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: Significant advancements have been made in the study of chromatin structure and function over the past fifty years but none as spectacular as those made in the last decade due to the development of novel techniques and the ability to sequence large stretches of DNA. In Chromatin Protocols, Second Edition, expert researchers delineate these cutting-edge techniques via step-by-step laboratory methods and protocols, which encompass a wide array of topics from the isolation of nucleosomes, assembly of nucleosomes and study of the basic chromatin structure to detailed analysis of histone modifications and chromatin function. Written in the highly successful Methods in Molecular BiologyTM series style, chapters include brief introductions to the subjects, lists of the necessary materials and reagents, readily reproducible protocols, and Notes sections which highlight tips on troubleshooting and avoiding known pitfalls. Comprehensive and up-to-date, Chromatin Protocols, Second Edition is a valuable tool for scientists studying various aspects of chromatin function and an ideal guide to aid in the development of new techniques as well as new ideas in the field of chromatin biology.
Download or read book Stem Cell Epigenetics written by and published by Academic Press. This book was released on 2020-08-07 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: Growing evidence suggests that epigenetic mechanisms play a central role in stem cell biology and are vital for determining gene expression during cellular differentiation and governing mammalian development. In Stem Cell Epigenetics, leading international researchers examine how chromatin regulation and bona fide epigenetic mechanisms underlie stem cell renewal and differentiation. Authors also explore how the diversity of cell types, including the extent revealed by single cell omic approaches, is achieved, and how such processes may be reversed or managed via epigenetic reprogramming. Topics discussed include chromatin in pluripotency, stem cells and DNA methylation, histone modifications in stem cells and differentiation, higher-order chromatin conformation in pluripotent cells, stem cells and cancer, epigenetics and disease modeling, brain organoids from pluripotent cells, transcriptional regulation in stem cells and differentiation, non-coding RNAs in pluripotency and early differentiation, and diseases caused by epigenetic alterations in stem cells. Additionally, the book discusses the potential implementation of stem cell epigenetics in drug discovery, regenerative medicine, and disease treatment. Stem Cell Epigenetics will provide researchers and physicians with a state-of-the-art map to orient across the frontiers of this fast-evolving field. Analyzes the role of epigenetics in embryonic stem cell regulation Indicates the epigenetic mechanisms involved in stem cell differentiation and highlights modifications and misregulations that may result in disease pathogenesis Examines the potential applications of stem cell epigenetics in therapeutic disease interventions and regenerative medicine, providing a foundation for researchers and physicians to bring this exciting and fast-evolving field into a clinical setting Features chapter contributions by leading international experts
Book Synopsis Hi-C Data Analysis by : Silvio Bicciato
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.
Book Synopsis Genome Organization And Function In The Cell Nucleus by : Karsten Rippe
Download or read book Genome Organization And Function In The Cell Nucleus written by Karsten Rippe and published by John Wiley & Sons. This book was released on 2011-12-19 with total page 597 pages. Available in PDF, EPUB and Kindle. Book excerpt: By way of its clear and logical structure, as well as abundant highresolution illustrations, this is a systematic survey of the players and pathways that control genome function in the mammalian cell nucleus. As such, this handbook and reference ties together recently gained knowledge from a variety of scientific disciplines and approaches, dissecting all major genomic events: transcription, replication, repair, recombination and chromosome segregation. A special emphasis is put on transcriptional control, including genome-wide interactions and non-coding RNAs, chromatin structure, epigenetics and nuclear organization. With its focus on fundamental mechanisms and the associated biomolecules, this will remain essential reading for years to come.
Book Synopsis Nuclear Architecture and Dynamics by : Christophe Lavelle
Download or read book Nuclear Architecture and Dynamics written by Christophe Lavelle and published by Academic Press. This book was released on 2017-10-27 with total page 620 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nuclear Architecture and Dynamics provides a definitive resource for (bio)physicists and molecular and cellular biologists whose research involves an understanding of the organization of the genome and the mechanisms of its proper reading, maintenance, and replication by the cell. This book brings together the biochemical and physical characteristics of genome organization, providing a relevant framework in which to interpret the control of gene expression and cell differentiation. It includes work from a group of international experts, including biologists, physicists, mathematicians, and bioinformaticians who have come together for a comprehensive presentation of the current developments in the nuclear dynamics and architecture field. The book provides the uninitiated with an entry point to a highly dynamic, but complex issue, and the expert with an opportunity to have a fresh look at the viewpoints advocated by researchers from different disciplines. Highlights the link between the (bio)chemistry and the (bio)physics of chromatin Deciphers the complex interplay between numerous biochemical factors at task in the nucleus and the physical state of chromatin Provides a collective view of the field by a large, diverse group of authors with both physics and biology backgrounds
Book Synopsis Transcriptional and Chromatin Regulation in Adaptive and Innate Immune Cells by : Keiko Ozato
Download or read book Transcriptional and Chromatin Regulation in Adaptive and Innate Immune Cells written by Keiko Ozato and published by Frontiers Media SA. This book was released on 2020-05-22 with total page 149 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription depends on an ordered sequence of events, starting with (i) setting of the enhancer and chromatin environment, (ii) assembly of DNA binding and general transcription factors, (iii) initiation, elongation, processing of mRNA and termination, followed by (iv) creation of epigenetic marks and memory formation. Highlighting the importance of these activities, more than 10% total genes are dedicated to regulating transcriptional mechanisms. This area of research is highly active and new insights are continuously being added to our knowledge. Cells of the immune system have unique features of gene regulation to support diverse tasks required for innate and adaptive immunity. Innate immunity involves the recognition of external infectious and noxious agents as well as internal cancer cell components, and the elimination of these agents by non-specific mechanisms. Adaptive immunity involves gene rearrangement to achieve highly specific T and B cell responses, imparting the capability of self and non-self discrimination. This requires transcription and epigenetic regulation. Adaptive immunity also employs epigenetic memory, enabling recapitulation of prior transcription. Recent advances in nuclear architecture, chromatin structure, and transcriptional regulation have provided new insights into immune responses. The increased understanding of these molecular mechanisms is now affording opportunities to improve therapeutic strategies for various diseases.
