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Nuclear Architecture and Dynamics, Volume 2 [Hardback]

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Edited by (Research Scientist, National Center for Scientific Research (CNRS), Principal Investigator, National Museum of Natural History, Paris, France), Edited by (Research Director, National Center for Research Science (CNRS), Principal Investigator, Un)
  • Formāts: Hardback, 618 pages, height x width: 235x191 mm, weight: 1450 g
  • Sērija : Translational Epigenetics
  • Izdošanas datums: 20-Oct-2017
  • Izdevniecība: Academic Press Inc
  • ISBN-10: 0128034807
  • ISBN-13: 9780128034804
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Nuclear Architecture and Dynamics, Volume 2Palielināt
  • Formāts: Hardback, 618 pages, height x width: 235x191 mm, weight: 1450 g
  • Sērija : Translational Epigenetics
  • Izdošanas datums: 20-Oct-2017
  • Izdevniecība: Academic Press Inc
  • ISBN-10: 0128034807
  • ISBN-13: 9780128034804
Citas grāmatas par šo tēmu:
Permanent link: https://www.kriso.lv/db/9780128034804.html
Keywords:

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

Papildus informācija

Provides a biophysical and biochemical framework in which to interpret the control of gene expression and cell differentiation
Section I Chromatin Organization and Dynamics
Chapter 1 DNA Mechanics
3(38)
John F. Marko
1.1 Basic Properties of DNA
3(6)
1.2 The Double Helix Is a Semiflexible Polymer
9(6)
1.3 Double-Helix Topology and Twisting Stiffness
15(13)
1.4 Beyond the Decoupled Harmonic Model of Double-Helix Elasticity
28(2)
1.5 Severe Deformations of the Double Helix
30(3)
1.6 Overview of DNA---Protein Interactions
33(8)
References
37(4)
Chapter 2 The Role of Nucleosome Positioning in Genome Function and Evolution
41(40)
Alain Arneodo
Guenola Drillon
Frangoise Argoul
Benjamin Audit
2.1 Introduction
41(3)
2.2 A Sequence-Dependent Physical Model of Nucleosome Occupancy
44(3)
2.3 Comparing In Vivo and In Vitro Primary Structures of Chromatin
47(5)
2.4 Functional Location of NIEBs in Saccharomyces cerevisiae
52(7)
2.5 NIEBs and Intrinsic Flanking Nucleosomes Are Widely Distributed Along Human Chromosomes
59(12)
2.6 Conclusion
71(10)
Acknowledgments
72(1)
References
72(9)
Chapter 3 DNA Supercoiling(omics)
81(20)
Laura Baranello
David Levens
Fedor Kouzine
3.1 Introduction
81(6)
3.2 Current Hot Spots
87(7)
3.3 Perspective
94(7)
References
95(6)
Chapter 4 Dynamic Chromatin Folding in the Cell
101(22)
Tadasu Nozaki
Damien F. Hudson
Sachiko Tamura
Kazuhiro Maeshima
4.1 Genomic DNA
101(1)
4.2 Nucleosome
102(2)
4.3 Chromatin Structure In Vitro
104(4)
4.4 Chromatin Structure In Vivo
108(2)
4.5 Liquid-Like Behavior of Chromatin
110(2)
4.6 Higher Order Chromatin Structure
112(3)
4.7 Mitotic Chromosome Formation
115(8)
Acknowledgments
116(1)
References
116(7)
Chapter 5 Mesoscale Modeling of Chromatin Fibers
123(26)
Gavin D. Bascom
Tamar Schlick
5.1 Introduction: The Chromatin Fiber Structure and Function
123(6)
5.2 Mesoscale Chromatin Modeling
129(8)
5.3 Applications
137(6)
5.4 Future Prospects
143(6)
Acknowledgments
144(1)
References
144(5)
Chapter 6 A Polymer Physics View on Universal and Sequence-Specific Aspects of Chromosome Folding
149(22)
Daniel Jost
Angela Rosa
Cedric Vaillant
Ralf Everaers
6.1 Introduction
149(1)
6.2 Experimental Insight on Nuclear Genome Organization: From DNA to TADs and Chromosome Territories
150(4)
6.3 Universal Aspects of Chromosome Folding: Polymer Theory
154(6)
6.4 Sequence-Specific Aspects of Chromosome Folding: Polymer Theory
160(4)
6.5 Discussion and Conclusions
164(7)
Acknowledgments
166(1)
References
167(4)
Chapter 7 Persistence of Long-Range Contacts at Insulators: Turnover Dynamics or Engaged Cohesin?
171(16)
Raphael Mourad
Olivier Cuvier
7.1 Enhancers, Promoters, and Insulators
171(1)
7.2 Insulator-Binding Proteins and Cofactors
172(3)
7.3 Barrier Insulators and Epigenetically Marked Chromatin Domains
175(2)
7.4 Persistence of Long-Range Contacts at Insulators: Equilibrium Dynamics or Deterministic Reactions?
177(10)
References
179(8)
Chapter 8 Long-Range Intranuclear Interactions
187(22)
Ivan Krivega
Ann Dean
8.1 Introduction
187(1)
8.2 Genome-Wide Long-Range Interactions
188(6)
8.3 Mechanisms of Establishing and Maintaining Local Long-Range Interactions
194(2)
8.4 Role of Alteration of 3D Organization in Disease
196(5)
8.5 Future Directions
201(8)
Acknowledgments
202(1)
References
202(7)
Chapter 9 The Multiple Effects of Molecular Crowding in the Cell Nucleus: From Molecular Dynamics to the Regulation of Nuclear Architecture
209(26)
Theo Lebeaupin
Rebecca Smith
Sebastien Huet
9.1 Introduction
209(3)
9.2 Macromolecular Crowding in the Nucleus: The Predictions of the Theoretical and In Vitro Data
212(6)
9.3 Current Experimental Evidences of the Impact of Crowding on Molecular Dynamics in the Cell Nucleus
218(4)
9.4 A Physiological Role for Macromolecular Crowding Inside the Nucleus?
222(3)
9.5 Conclusions and Future Challenges
225(10)
References
226(9)
Section II Nuclear Envelope, Nuclear Bodies, and Nucleocytoplasmic Trafficking
Chapter 10 Nuclear Bodies
235(22)
Iain A. Sawyer
Miroslav Dundr
10.1 Introduction
235(2)
10.2 Nuclear Body Assembly
237(2)
10.3 Why Build a Nuclear Body?
239(2)
10.4 List of Nuclear Bodies
241(8)
10.5 Recent Developments---Biophysical Examination of NB Function and Assembly
249(1)
10.6 Clinical Relevance
250(1)
10.7 Concluding Remarks
251(6)
Acknowledgments
252(1)
References
252(5)
Chapter 11 Nucleolus: The Consummate Nuclear Body
257(26)
Laura Trinkle-Mulcahy
11.1 A Brief History
257(5)
11.2 Ribosome Biogenesis
262(1)
11.3 Ribosomal Genes and NORs
263(2)
11.4 Nucleolar Plasticity
265(4)
11.5 Building a Nucleolus
269(2)
11.6 Physical Properties of Nucleoli
271(1)
11.7 Conclusion
272(11)
Acknowledgments
272(1)
References
273(10)
Chapter 12 Transcription Factories as Spatial and Functional Organization Nodes
283(14)
Konstantinos Sofiadis
Argyris Papantonis
12.1 Genome Organization in Respect to Transcriptional Activity
283(2)
12.2 An Operational Definition for Transcription Factories
285(1)
12.3 Resolving Earlier Controversy About Transcription Factories
286(2)
12.4 Physical Properties of Transcription Factories
288(1)
12.5 Functional Properties of Transcription Factories
289(2)
12.6 The Loop Extrusion Model and Factories
291(1)
12.7 Conclusion and Outlook
292(5)
References
292(4)
Further Reading
296(1)
Chapter 13 Polycomb Bodies
297(24)
Louise Matheson
Sarah Elderkin
13.1 Diversity of Polycomb Repressive Complexes
297(2)
13.2 Polycomb Repressive Complex Recruitment
299(1)
13.3 Polycomb Bodies: A Historical View
300(1)
13.4 Polycomb Body Composition and Distribution
301(1)
13.5 Polycomb Body Dynamics
302(2)
13.6 Polycomb Body Formation
304(3)
13.7 Polycomb Bodies, Nuclear Architecture, and Gene Regulation
307(6)
13.8 Specialized Functions of Polycomb Bodies
313(1)
13.9 Concluding Remarks
314(7)
References
315(6)
Chapter 14 The Nuclear Lamina and Genome Organization
321(24)
Marie-Cecile Gaillard
Karen L. Reddy
14.1 The Nuclear Lamina and Nuclear Envelope
321(2)
14.2 The Lamins
323(1)
14.3 The Lamins Directly Interact With INM Proteins
324(1)
14.4 The Lamina Links the Cytoskeleton With the Nucleus
325(1)
14.5 The Nuclear Lamina is Dynamic Through Mitosis
326(1)
14.6 The Nuclear Lamina is a Developmentally Dynamic Structure
327(1)
14.7 Lamina-Associated Domains
327(3)
14.8 Lamins and INM Proteins in LAD Organization
330(1)
14.9 The INM/Lamina as a Transcriptionally Repressive Compartment
330(1)
14.10 Chromatin and LAD Organization
331(2)
14.11 LADs and Genome Organization
333(1)
14.12 Involvement of Nuclear Periphery in Human Diseases and Aging
333(3)
14.13 Perspectives
336(9)
References
337(8)
Chapter 15 Actin in the Cell Nucleus
345(24)
Tomas Venit
Xin Xie
Piergiorgio Percipalle
15.1 Actin and Myosin Regulate Transcription by Eukaryotic RNA Polymerases
345(4)
15.2 Cotranscriptional Association of Actin With Ribonucleoprotein Complexes
349(3)
15.3 Actin From Gene to Polyribosomes: What Next?
352(1)
15.4 Actin-Containing Chromatin Remodeling Complexes
353(2)
15.5 Potential Roles of Actin in Chromatin-Remodeling Complexes
355(3)
15.6 Actin and Myosin in the Long-Range Movement of Chromosome Sites
358(1)
15.7 Actin as Part of Nucleoskeleton
358(1)
15.8 Actin, ARPs, and ABPs in DNA Damage Repair
359(1)
15.9 Concluding Remarks
360(9)
References
361(8)
Chapter 16 Nuclear Pores and the Genome
369(18)
Maya Capelson
16.1 Introduction
369(1)
16.2 NPC Structure and Assembly
370(3)
16.3 Chromatin-Binding Roles of the NPC in Transcriptional Regulation
373(3)
16.4 NPCs and Maintenance of Genome Integrity
376(3)
16.5 Perspectives
379(8)
References
380(7)
Chapter 17 Protein Transport Between the Nucleus and Cytoplasm
387(20)
Yoichi Miyamoto
Yoshihiro Yoneda
Masahiro Oka
17.1 Introduction
387(1)
17.2 Nuclear Pore Complex
387(2)
17.3 Signals for Nuclear Import and Export
389(1)
17.4 Ran Gradient
390(1)
17.5 Molecular Mechanisms of Nuclear Protein Import and Export
391(1)
17.6 Importin β Family, Transporters of Nuclear-Cytoplasmic Transport
392(1)
17.7 Importin α, a cNLS Receptor Molecule
393(1)
17.8 Physiological Processes and Nuclear Transport Factors
394(2)
17.9 Conclusions
396(11)
Acknowledgments
397(1)
References
397(10)
Section III Main Nuclear Functions
Chapter 18 Replicating Chromatin in the Eukaryotic Genome
407(28)
Molly R. Gordon
Daniel A. Bartlett
David M. Gilbert
18.1 Introduction
407(1)
18.2 Toolkit: Studying Replication of Chromatin
408(1)
18.3 Replication Initiation Depends on Chromatin Context
409(10)
18.4 Chromatin Folding and Replication Timing Regulation
419(3)
18.5 Replication Elongation: Making and Breaking Chromatin
422(2)
18.6 Chromatin Maturation
424(1)
18.7 Replication Termination
425(1)
18.8 Concluding Remarks
426(9)
Acknowledgments
427(1)
References
427(7)
Further Reading
434(1)
Chapter 19 Promoter--Enhancer Looping and Regulatory Neighborhoods: Gene Regulation in the Framework of Topologically Associating Domains
435(22)
Charbel Souaid
Sebastien Bloyer
Daan Noordermeer
19.1 Gene Regulation and DNA Looping Between Regulatory Elements
435(6)
19.2 Gene Looping Within the Framework of TADs
441(7)
19.3 DNA Looping and TAD Function as Regulators in Development and Disease
448(3)
19.4 Conclusions and Outlook
451(6)
Acknowledgments
451(1)
References
452(5)
Chapter 20 Sailing the Hi-C's: Benefits and Remaining Challenges in Mapping Chromatin Interactions
457(18)
Yousra B. Zouari
Anne M. Molitor
Tom Sexton
20.1 Detecting Chromatin Interactions: From 3C to Hi-C
457(2)
20.2 What Can We Learn From Hi-C About Chromosome Folding?
459(3)
20.3 Other Applications of Hi-C
462(1)
20.4 Limitations of Hi-C
463(5)
20.5 Concluding Remarks
468(7)
References
468(7)
Chapter 21 Chromatin Folding and Recombination
475(18)
Valentino Snetkova
Jane A. Skok
21.1 Introduction
475(1)
21.2 RAG Targeting
476(1)
21.3 Accessibility of the Antigen Receptor Loci
477(1)
21.4 Allelic Exclusion
478(1)
21.5 Changes in Antigen Receptor Locus Architecture
479(2)
21.6 Factors That Contribute to Locus Contraction
481(1)
21.7 Insulator Elements and Their Role in Generating a Balanced V Gene Repertoire
482(3)
21.8 RAG Off-Target Activity is Restricted Within a Loop
485(2)
21.9 Concluding Comments and Future Directions
487(6)
Acknowledgments
489(1)
References
489(4)
Chapter 22 Altered Nucleus and Disease
493(22)
Josette M. Northcott
Valerie M. Weaver
22.1 Introduction
493(1)
22.2 Cancer-Associated Alterations to Nuclear Morphology
494(2)
22.3 Nuclear Architecture: The Role of Proteins at the Nuclear Periphery
496(6)
22.4 Chromatin Organization: A Means of Maintaining Genomic Stability
502(2)
22.5 Nuclear Bodies: Compartmentalization of Nuclear Processes
504(2)
22.6 Current Therapeutics and Prospective Targets
506(1)
22.7 Summary
507(8)
References
507(8)
Section IV Specific Features of Nuclear Organization in Main Model Organisms
Chapter 23 Yeast Nucleus: A Model for Chromatin Folding Principles
515(18)
Etienne Almayrac
Emmanuelle Fabre
23.1 Yeast Nuclear Anchoring Features
515(3)
23.2 Models Emerged From Polymer Physics
518(1)
23.3 Chromosome Folding: Double Strand Break Outcomes
519(2)
23.4 Chromosome Refolding Upon Physiological Changes
521(3)
23.5 Chromatin Dynamics, Cause, and Consequences
524(2)
23.6 Concluding Remarks and Perspectives
526(7)
Acknowledgments
527(1)
References
527(6)
Chapter 24 Chromosomes and Chromatin in the Nematode Nucleus
533(24)
Adriana Gonzalez-Sandoval
Peter Meister
24.1 Introduction
533(1)
24.2 Nematodes: A Short Life Cycle and Easy Genetics
533(2)
24.3 DNA and Chromatin Modifications
535(5)
24.4 Large-Scale Chromosome Organization
540(9)
24.5 The Special Case of the X Chromosome: Dosage Compensation, Chromatin Composition, and Large-Scale Chromosome Organization
549(2)
24.6 Concluding Remarks
551(6)
Acknowledgments
551(1)
References
551(6)
Chapter 25 Nuclear Dynamics at Specific Cell Cycle Stages in the Slime Mold Physarum polycephalum
557(12)
Christophe Thiriet
25.1 The Life Cycle of Physarum
558(1)
25.2 The Diploid Stages
558(1)
25.3 The Haploid Stages
559(1)
25.4 Physarum Nucleus
559(1)
25.5 Internalization of Exogenous Proteins
560(1)
25.6 Replication Coupled Chromatin Assembly
561(2)
25.7 Chromatin Dynamics in Transcription
563(2)
25.8 Perspective
565(4)
Acknowledgments
566(1)
References
566(3)
Index 569
Christophe Lavelle, Volume Editor, is a research scientist at the CNRS (National Center for Scientific Research), principal investigator at the National Museum of Natural History in Paris. His studies mostly concern the biophysical properties of DNA and dynamical processes at task in the nucleus. He teaches biophysics and epigenetics in several universities (Paris VI, Paris VII, Aix-Marseille, Lyon, Lille, Toulouse) and is a member of the American and the French Biophysical Societies. Jean-Marc Victor, Volume Editor, is a research director at the CNRS, principal investigator at the University Pierre et Marie Curie - Paris VI (part of Sorbonne University). His studies mostly concern the physics of chromosomes (theory and simulations) and the modeling of nuclear processes, with special attention to epigenetics and chronic diseases.