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.
1. Cover image - p. Cover 2. Title page - p. iii 3. Table of Contents - p. iii 4. Copyright - p. iv 5. List of Contributors - p. xvii 6. Preface - p. xxi 7. I: Chromatin Organization and Dynamics - p. xxi 8. 1. DNA Mechanics - p. 3 9. 2. The Role of Nucleosome Positioning in Genome Function and Evolution - p. 41 10. 3. DNA Supercoiling(omics) - p. 81 11. 4. Dynamic Chromatin Folding in the Cell - p. 101 12. 5. Mesoscale Modeling of Chromatin Fibers - p. 123 13. 6. A Polymer Physics View on Universal and Sequence-Specific Aspects of Chromosome Folding - p. 149 14. 7. Persistence of Long-Range Contacts at Insulators: Turnover Dynamics or Engaged Cohesin? - p. 171 15. 8. Long-Range Intranuclear Interactions - p. 187 16. 9. The Multiple Effects of Molecular Crowding in the Cell Nucleus: From Molecular Dynamics to the Regulation of Nuclear Architecture - p. 209 17. II: Nuclear Envelope, Nuclear Bodies, and Nucleocytoplasmic Trafficking - p. 226 18. 10. Nuclear Bodies - p. 235 19. 11. Nucleolus: The Consummate Nuclear Body - p. 257 20. 12. Transcription Factories as Spatial and Functional Organization Nodes - p. 283 21. 13. Polycomb Bodies - p. 297 22. 14. The Nuclear Lamina and Genome Organization - p. 321 23. 15. Actin in the Cell Nucleus - p. 345 24. 16. Nuclear Pores and the Genome - p. 369 25. 17. Protein Transport Between the Nucleus and Cytoplasm - p. 387 26. III: Main Nuclear Functions - p. 397 27. 18. Replicating Chromatin in the Eukaryotic Genome - p. 407 28. 19. Promoter–Enhancer Looping and Regulatory Neighborhoods: Gene Regulation in the Framework of Topologically Associating Domains - p. 435 29. 20. Sailing the Hi-C’s: Benefits and Remaining Challenges in Mapping Chromatin Interactions - p. 457 30. 21. Chromatin Folding and Recombination - p. 475 31. 22. Altered Nucleus and Disease - p. 493 32. IV: Specific Features of Nuclear Organization in Main Model Organisms - p. 507 33. 23. Yeast Nucleus: A Model for Chromatin Folding Principles - p. 515 34. 24. Chromosomes and Chromatin in the Nematode Nucleus - p. 533 35. 25. Nuclear Dynamics at Specific Cell Cycle Stages in the Slime Mold Physarum polycephalum - p. 557 36. Index - p. 569
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.
1. Cover image - p. Cover 2. Title page - p. iii 3. Table of Contents - p. iii 4. Copyright - p. iv 5. List of Contributors - p. xvii 6. Preface - p. xxi 7. I: Chromatin Organization and Dynamics - p. xxi 8. 1. DNA Mechanics - p. 3 9. 2. The Role of Nucleosome Positioning in Genome Function and Evolution - p. 41 10. 3. DNA Supercoiling(omics) - p. 81 11. 4. Dynamic Chromatin Folding in the Cell - p. 101 12. 5. Mesoscale Modeling of Chromatin Fibers - p. 123 13. 6. A Polymer Physics View on Universal and Sequence-Specific Aspects of Chromosome Folding - p. 149 14. 7. Persistence of Long-Range Contacts at Insulators: Turnover Dynamics or Engaged Cohesin? - p. 171 15. 8. Long-Range Intranuclear Interactions - p. 187 16. 9. The Multiple Effects of Molecular Crowding in the Cell Nucleus: From Molecular Dynamics to the Regulation of Nuclear Architecture - p. 209 17. II: Nuclear Envelope, Nuclear Bodies, and Nucleocytoplasmic Trafficking - p. 226 18. 10. Nuclear Bodies - p. 235 19. 11. Nucleolus: The Consummate Nuclear Body - p. 257 20. 12. Transcription Factories as Spatial and Functional Organization Nodes - p. 283 21. 13. Polycomb Bodies - p. 297 22. 14. The Nuclear Lamina and Genome Organization - p. 321 23. 15. Actin in the Cell Nucleus - p. 345 24. 16. Nuclear Pores and the Genome - p. 369 25. 17. Protein Transport Between the Nucleus and Cytoplasm - p. 387 26. III: Main Nuclear Functions - p. 397 27. 18. Replicating Chromatin in the Eukaryotic Genome - p. 407 28. 19. Promoter–Enhancer Looping and Regulatory Neighborhoods: Gene Regulation in the Framework of Topologically Associating Domains - p. 435 29. 20. Sailing the Hi-C’s: Benefits and Remaining Challenges in Mapping Chromatin Interactions - p. 457 30. 21. Chromatin Folding and Recombination - p. 475 31. 22. Altered Nucleus and Disease - p. 493 32. IV: Specific Features of Nuclear Organization in Main Model Organisms - p. 507 33. 23. Yeast Nucleus: A Model for Chromatin Folding Principles - p. 515 34. 24. Chromosomes and Chromatin in the Nematode Nucleus - p. 533 35. 25. Nuclear Dynamics at Specific Cell Cycle Stages in the Slime Mold Physarum polycephalum - p. 557 36. Index - p. 569
