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

• Main Author: Prakash, Kirti (Author)
• Format: Electronic eBook
• Language: English
• Published: Cham, Switzerland : Springer, 2017.
• Series: Springer theses.
• Subjects: Chromatin.; elektronické knihy; electronic books
• ISBN: 9783319521831; 9783319521824
• Physical Description: 1 online resource : illustrations (some color)

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 F...

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.