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Preface xix
List of Contributors xxi
1 Deciphering DNA Sequence Information 1
Mark Kaganovich and Michael Snyder
1.1 Introduction 1
1.2 Genes and Transcribed Regions 1
1.3 Non-Coding Genomic Elements 4
1.4 Regulatory Information 10
1.5 Individual Genetic Polymorphisms and Their Effect on Gene Expression 16
1.6 Conclusion 16
2 DNA Methylation 21
Carina Frauer, Fabio Spada, and Heinrich Leonhardt
2.1 Introduction 21
2.2 Eukaryotic DNA Methyltransferases 24
2.3 Distribution of 5-Methylcytosine in the Mammalian Genome 27
2.4 Control of Gene Expression by DNA Methylation 31
2.5 DNA Demethylation 37
3 Nucleosomes as Control Elements for Accessing the Genome 55
Mekonnen Lemma Dechassa and Karolin Luger
3.1 Introduction and Basic Terminology 55
3.2 Nucleosomes are the Building Blocks of Chromatin 56
3.3 Nucleosomes Are Dynamic Macromolecular Assemblies 63
3.4 Histone Variants and Their Effect on Nucleosome Structure and Dynamics 66
3.5 Histone Modifications in Nucleosome and Chromatin Structure 68
3.6 DNA Sequence and Nucleosome Positioning 70
3.7 Histone Chaperones and Chromatin Dynamics 73
3.8 Outlook and Concluding Remarks 75
4 Histone Modifications and Their Role as Epigenetic Marks 89
Karl Nightingale
4.1 The Complexity of Histone Modifications 89
4.2 Regulating Histone Modifications in Chromatin 93
4.3 The “Histone Code” Hypothesis 95
4.4 Exploiting the Complexity of the Histone Code: “Crosstalk” Between Different Modifications 98
4.5 Are Histone Modifications Heritable Epigenetic Marks? 104
4.6 Conclusions 106
5 Chromatin Remodeling and Nucleosome Positioning 111
Gernot Lañgst, Vladimir B. Teif, and Karsten Rippe
5.1 Introduction 111
5.2 Chromatin Remodeling Complexes 112
5.3 Mechanisms of Nucleosome Translocations 115
5.4 Positioning Nucleosomes in the Genome 118
5.5 Gene Regulation via Nucleosome Positioning 124
5.6 Conclusions 127
6 The Folding of the Nucleosome Chain 139
Karsten Rippe
6.1 Introduction 139
6.2 Experimental Systems 140
6.3 Nucleosome–Nucleosome Interactions 142
6.4 DNA Interactions with the Histone Octamer Protein Core 145
6.5 Architectural Chromosomal Proteins and Chromatin States 147
6.6 Chromatin Fiber Conformations 150
6.7 Conclusions 154
7 The Crowded Environment of the Genome 169
Ron Hancock
7.1 Introduction 169
7.2 Basics 169
7.3 Physicochemical Parameters of the Genome’s Environment 171
7.4 Implications of a Crowded Environment for the Conformation of the Interphase Genome 171
7.5 Assembly and Localization of Macromolecular Machines for Genome Transcription and Replication 175
7.6 The Environment of the Genome during Mitosis 177
7.7 Effects of a Crowded Environment on Searching for Targets in the Genome 178
7.8 The Relative Importance of Entropic and Ionic Interactions for the Conformations and Interactions of Macromolecules in the Nucleus 179
7.9 The Evolution of Genomes 180
8 The Nuclear Lamina as a Chromatin Organizer 185
Nikolaj Zuleger and Eric C. Schirmer
8.1 Introduction 185
8.2 Genome Organization with Respect to the Nuclear Periphery 187
8.3 Interactions between NE Proteins and Chromatin Proteins/Chromatin Regulatory Proteins 190
8.4 Mechanisms Directing Changes in Genome Organization during Development 193
8.5 Gene Regulation as a Consequence of Peripheral Positioning 198
8.6 Peripheral Chromatin Organization and Disease 201
8.7 Closing Remarks 203
9 Three-Dimensional Architecture of Genomes 211
Job Dekker
9.1 Introduction 211
9.3 Chromosome Architecture as Seen by 3C-Based Assays 218
9.4 3C-Based Data and Single Cell Observations 226
9.5 Towards an Integrated 3C-Based View of Genome Architecture 227
10 Transcriptional Initiation: Frequency, Bursting, and Transcription Factories 235
Kieran Finan and Peter R. Cook
10.1 Transcription in Mammalian Nuclei 235
10.2 Transcription Is an Infrequent Event 236
10.3 Transcription Is Noisy 238
10.4 What Causes “Bursting”? 245
10.5 Conclusion 250
11 Processing of mRNA and Quality Control 255
Ute Schmidt and Edouard Bertrand
11.1 Introduction 255
11.2 Biosynthesis of Messenger RNA 255
11.3 Nuclear Quality Control 265
11.4 Cytoplasmic Messenger RNA Quality Control: Nonsense-Mediated Decay, No-Go and Non-Stop Decay 268
11.5 Concluding Remarks 273
12 The Nucleolus 279
Saskia Hutten, Belinda J. Westman, Franc-ois-Michel Boisvert, Silvana van Koningsbruggen, and Angus I. Lamond
12.1 Introduction 279
12.2 The Nucleolus and Its DNA 280
12.3 The Nucleolus and RNPs: Temporary Visitors or Permanent Residents? 285
12.4 The Nucleolar Proteome 292
12.5 Concluding Remarks 295
13 Non-Coding RNAs as Regulators of Transcription and Genome Organization 309
Katalin Fejes Toth and Gregory Hannon
13.1 Introduction 309
13.2 Classification of Non-Coding RNAs 311
13.3 Small Regulatory RNAs and Their Diverse Nuclear Functions 314
13.4 ncRNAs in Dosage Compensation 324
13.5 Developmental Regulation of Hox Clusters by Cis- and Trans-Acting ncRNAs 328
13.6 Mechanisms of Transcriptional Regulation by Long ncRNAs 330
13.7 Conclusions 338
14 RNA Networks as Digital Control Circuits of Nuclear Functions 353
John S. Mattick
14.1 Introduction 353
14.2 The Information Content of the Genome 353
14.3 The Hidden Layer of Developmentally Expressed Non-Coding RNAs 354
14.4 RNA Control of Nuclear Functions 355
14.5 RNA as the Adaptor in Digital–Analog Transactions 356
14.6 RNA as the Substrate for Environment–Epigenome Interactions 357
14.7 Conclusion 358
15 DNA Replication and Inheritance of Epigenetic States 365
Armelle Corpet and Geneviève Almouzni
15.1 Replication in a Chromatin Context: Basic Issues and Principles 365
15.2 Duplication of Nucleosome Organization 368
15.3 Maintenance of Epigenetic Marks and Post-translational Modifications 375
15.4 Concluding Remarks 383
16 Interplay and Quality Control of DNA Damage Repair Mechanisms 395
Berina Eppink, Jeroen Essers and Roland Kanaar
16.1 Introduction 395
16.2 DNA Repair Pathways 396
16.3 Repairing DSBs 400
16.4 Repair during Replication 404
16.5 Interplay and Quality Control during DNA Damage Repair 409
16.6 Applications of Mechanistic Insight in DNA Repair in Anti-Cancer Treatment 410
17 Higher Order Chromatin Organization and Dynamics 417
Hilmar Strickfaden, Thomas Cremer, and Karsten Rippe
17.1 Introduction 417
17.2 Higher Order Chromatin Organization: From 10-nm Thick Nucleosome Chains to Chromosome Territories 418
17.3 Genome Accessibility 424
17.4 Mobility of Chromosomal Loci and Nuclear Bodies 426
17.5 Mitosis Causes Drastic Changes of Chromosome Territory Proximity Patterns in Cycling Cells 429
17.6 Large-Scale Chromatin Dynamics in Nuclei of Cycling and Post-Mitotic Cells 431
17.7 Considerations on Possible Mechanisms of Large-Scale Chromatin Dynamics 434
18 The Mitotic Chromosome: Structure and Mechanics 449
John F. Marko
18.1 Introduction 449
18.2 Structural Components of Mitotic Chromosomes 450
18.3 Large-Scale Organization of Mitotic Chromosomes 457
18.4 Mechanics of Mitotic Chromosomes 459
18.5 Molecular Connectivity of Mitotic Chromosomes 465
18.6 A Model for Mitotic Chromosome Structure and Function 468
18.7 Open Questions 474
19 Meiotic Chromosome Dynamics 487
Nancy Kleckner, Liangran Zhang, Beth Weiner, and Denise Zickler
19.1 Introduction 487
19.2 Recombination at the DNA Level 494
19.3 Coordination between Recombination and Chromosome Dynamics 500
19.4 Homologous Chromosome Pairing 507
19.5 Meiotic Recombination as a Paradigm for Spatial Patterning along Chromosomes 515
20 Understanding Genome Function: Quantitative Modeling of Chromatin Folding and Chromatin-Associated Processes 535
Mariliis Tark-Dame, Martijn S. Luijsterburg, Dieter W. Heermann and Roel van Driel
20.1 Modeling of Genome Functioning 535
20.2 Large-Scale Chromatin Folding 536
20.3 Assembly of Chromatin-Associated Multiprotein Complexes 543
20.4 Outlook 548
Index 557
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Add Genome Organization And Function In The Cell Nucleus, 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 toge, Genome Organization And Function In The Cell Nucleus to the inventory that you are selling on WonderClubX
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Add Genome Organization And Function In The Cell Nucleus, 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 toge, Genome Organization And Function In The Cell Nucleus to your collection on WonderClub |