Chromatin architecture : advances from high-resolution single molecule DNA imaging /

Chromatin architecture : advances from high-resolution single molecule DNA imaging /

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Bibliographic Details
Author / Creator:Prakash, Kirti, author.
Imprint:Cham, Switzerland : Springer, 2017.
Description:1 online resource : illustrations (some color)
Language:English
Series:Springer theses
Springer theses.
Subject:
Chromatin.
Chromatin.
Chromatin.
Electronic book.
Format: E-Resource Book
URL for this record:http://pi.lib.uchicago.edu/1001/cat/bib/11271908
Hidden Bibliographic Details
ISBN:9783319521831
3319521837
9783319521824
3319521829
Digital file characteristics:text file PDF
Notes:"Doctoral thesis accepted by Institute of Molecular Biology, Mainz and Heidelberg University, Germany."
Includes bibliographical references.
Online resource; title from PDF title page (SpringerLink, viewed March 1, 2017).
Summary: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 chromatinℓ́ℓs 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.
Other form:Print version: Prakash, Kirti. Chromatin architecture. Cham, Switzerland : Springer, 2017 9783319521824 3319521829
Standard no.:10.1007/978-3-319-52183-1
Table of Contents:
  • Supervisor's Foreword; Preface; Parts of this thesis have been published in the following journal articles; In Peer-Reviewed Journals; In Conferences; Acknowledgements; Contents; Abbreviations; List of Figures; 1 A Condensed History of Chromatin Research; 1.1 The Early Research on the Nucleus and Chromatin; 1.2 Chromatin Bares Information: The Chromosomes #x83;; 1.3 Chromatin as a Decision Center of the Cellular Factory: The Golden #x83;; 1.4 Chromatin as a Highly Structured System: Genomic Data, Localisation #x83;; 1.5 The Substratum of Chromatin Memory: Epigenetic Regulation.
  • 1.6 Fine-Scale Chromatin Architecture: A New Modelling Area1.7 Conclusion; References; 2 Investigating Chromatin Organisation Using Single Molecule Localisation Microscopy; 2.1 Introduction; 2.2 Single-Molecule Localization Microscopy: State-of-the-Art; 2.2.1 Principle of SMLM; 2.2.2 The Different SMLM Methods: A Historical Perspective; 2.3 Application of SMLM to Image Chromatin; 2.3.1 The Tao of SMLM; 2.3.2 Importance of a Good Localization Precision in Order to Improve Resolution; 2.3.3 Importance of High Signal Density to Improve Signal-to-Noise Ratio.
  • 2.3.4 Limitations of Previous Approaches to Study Chromatin Organisation 2.4 A Method to Reach High Labelling Density of Chromatin with SMLM; 2.4.1 Theory of DNA Dye Fluorescence; 2.4.2 Adapting Study of DNA Dyes Fluorescence to SMLM; 2.4.3 Optimization of the Photoconversion Process; 2.4.4 Optimization of the Buffer Conditions; 2.4.5 Multicolor Imaging with DNA; 2.4.6 A Summary of Various Approaches Used to Study DNA with SMLM; 2.5 SMLM Microscope Design and Imaging Pipeline; 2.5.1 Sample Preparation for SMLM; 2.5.2 Imaging Medium; 2.6 Data Acquisition for SMLM.
  • 2.7 Data Reconstruction for SMLM2.7.1 Spot Finding for SMLM; 2.7.2 Drift Correction Algorithms for SMLM; 2.7.3 Data Visualisation for SMLM; 2.7.4 Data Analysis for SMLM; 2.8 Some Further Considerations for Localisation Microscopy; 2.8.1 Artefacts in Localisation Microscopy; 2.8.2 Difference Between Localisation Precision and Accuracy; 2.9 Summary; References; 3 Structure, Function and Dynamics of Chromatin; 3.1 Introduction; 3.2 The Hierarchical Organisation of Chromatin; 3.2.1 Chromosome Territories (Scale: 1000
  • 2000 nm); 3.2.2 Sub-chromosomal Domains (Scale: 500
  • 1000 nm).
  • 3.2.3 Chromatin Domains (Scale: 100
  • 400 nm)3.2.4 Chromatin Fibres (Scale: 30
  • 100 nm); 3.2.5 A Cluster-on-a-String Model to Describe the Fibre/Domain Transition; 3.2.6 Nucleosome Domains (Scale: 10
  • 30 nm); 3.2.7 Inference of Further Intermediate Chromatin Structures Using Local Chromatin Density Maps; 3.2.8 Hierarchical Organisation of Chromatin Structure; 3.3 The Dynamics of Chromatin; 3.3.1 Contrasting Arrangement of eu- and Hetero-Chromatin Inside the Cell Nucleus; 3.3.2 Classifier Identifies Intermediate States Between eu- and Heterochromatin Regions in Differentiated Cells.

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