Every species has to preserve the integrity of its genome to ensure faithful passage of genetic information to the progeny. At the same time, there are times during the life of the organism and population in general when a fine balance in genome stability and diversification has to be made to benefit the survival of the species. Genome Stability teaches the reader how various species maintain this fine balance in genome stability and genome diversification in response to their environments.
Genome Stability covers a wide range of topics, including the genome stability of DNA/RNA viruses, prokaryotes, single cell eukaryotes, lower multicellular eukaryotes and mammals. Topics also include major DNA repair mechanisms, the role of chromatin in genome stability, human diseases associated with genome instability as well as changes in genome stability in response to aging. Finally, Genome Stability covers how epigenetic factors contribute to genome stability and how the species pass the memory of the encounters to the progeny, thus influencing the genome of the progeny in an indirect manner. This volume is an essential resource for geneticists, epigeneticists, and molecular biologists who are looking to gain a deeper understanding of this rapidly-expanding field, and can also be of great use to advanced students who are looking to gain additional expertise in genome stability.
1. Introduction - p. xix 2. Chapter 1. Genome Stability: An Evolutionary Perspective - p. 1 3. Section I. Genome Instability of Viruses - p. 18 4. Chapter 2. Genetic Instability of RNA Viruses - p. 21 5. Chapter 3. Genome Instability in DNA Viruses - p. 37 6. Section II. Genome Instability in Bacteria and Archaea - p. 47 7. Chapter 4. Genome Instability in Bacteria and Archaea: Strategies for Maintaining Genome Stability - p. 51 8. Chapter 5. Genome Instability in Bacteria: Causes and Consequences - p. 69 9. Chapter 6. CRISPR: Bacteria Immune System - p. 87 10. Section III. Genome Stability of Unicellular Eukaryotes - p. 98 11. Chapter 7. From Micronucleus to Macronucleus: Programmed DNA Rearrangement Processes in Ciliates Are Regulated Epigenetically by Small and Long Noncoding RNA Molecules - p. 101 12. Chapter 8. Homologous Recombination and Nonhomologous End-Joining Repair in Yeast - p. 117 13. Section IV. Genome Stability in Multicellular Eukaryotes - p. 135 14. Chapter 9. Meiotic and Mitotic Recombination: First in Flies - p. 139 15. Chapter 10. Genome Stability in Drosophila: Mismatch Repair and Genome Stability - p. 155 16. Chapter 11. Genome Stability in Caenorhabditis elegans - p. 163 17. 1. Introduction - p. 163 18. 2. The Caenorhabditis elegans Model - p. 164 19. 3. Powerful Genetic Tools to Explore DDR Dynamics - p. 164 20. 4. Genotoxic Agents for DNA Damage Induction - p. 166 21. 5. Methods for DNA Damage Detection - p. 166 22. 6. Excision Repair - p. 167 23. 7. Mismatch Repair - p. 170 24. 8. Double-Strand Break Repair in C. elegans - p. 170 25. 9. DNA-Damage Checkpoints - p. 175 26. 10. Concluding Remarks - p. 177 27. Glossary - p. 177 28. List of Abbreviations - p. 179 29. Chapter 12. Genetic Engineering of Plants Using Zn Fingers, TALENs, and CRISPRs - p. 187 30. Chapter 13. Plant Genome Stability: General Mechanisms - p. 203 31. Section V. Genome Stability in Mammals - p. 223 32. Chapter 14. Cell-Cycle Control and DNA-Damage Signaling in Mammals - p. 227 33. Chapter 15. The Role of p53/p21/p16 in DNA-Damage Signaling and DNA Repair - p. 243 34. Chapter 16. Roles of RAD18 in DNA Replication and Postreplication Repair - p. 257 35. Chapter 17. Base Excision Repair and Nucleotide Excision Repair - p. 275 36. 1. General Overview and Historical Perspectives of Two DNA Excision-Repair Pathways, BER and NER - p. 275 37. 2. Mammalian BER - p. 276 38. 3. Mammalian NER - p. 283 39. 4. Biological Implications Beyond DNA Damage and Repair - p. 291 40. 5. Interplay Between NER and BER: The Key Role of the DNA-Damage Response for Prevention of Cellular Degeneration - p. 291 41. 6. Concluding Remarks - p. 293 42. Glossary - p. 293 43. List of Abbreviations - p. 294 44. Chapter 18. DNA Mismatch Repair in Mammals - p. 303 45. Chapter 19. Repair of Double-Strand Breaks by Nonhomologous End Joining: Its Components and Their Function - p. 321 46. Chapter 20. Double-Strand Break Repair: Homologous Recombination in Mammalian Cells - p. 337 47. Chapter 21. Telomere Maintenance and Genome Stability - p. 353 48. Chapter 22. The Relationship Between Checkpoint Adaptation and Mitotic Catastrophe in Genomic Changes in Cancer Cells - p. 373 49. Chapter 23. Chromatin, Nuclear Organization, and Genome Stability in Mammals - p. 391 50. Chapter 24. Role of DNA Methylation in Genome Stability - p. 409 51. Chapter 25. Noncoding RNAs in Genome Integrity - p. 425 52. Section VI. Human Diseases Associated With Genome Instability - p. 443 53. Chapter 26. Human Diseases Associated With Genome Instability - p. 447 54. Chapter 27. Cancer and Genomic Instability - p. 463 55. Chapter 28. Chromatin Modifications in DNA Repair and Cancer - p. 487 56. Chapter 29. Genomic Instability and Aging: Causes and Consequences - p. 511 57. Chapter 30. Nucleolar Contributions to DNA-Damage Response and Genomic (In)Stability in the Nervous System - p. 527 58. Section VII. Effect of Environment on Genome Stability - p. 539 59. Chapter 31. Diet and Nutrition - p. 543 60. Chapter 32. Chemical Carcinogens and Their Effect on Genome and Epigenome Stability - p. 555 61. Chapter 33. Environmental Sources of Ionizing Radiation and Their Health Consequences - p. 569 62. Section VIII. Bystander and Transgenerational Effects – Epigenetic Perspective - p. 581 63. Chapter 34. Sins of Fathers Through a Scientific Lens: Transgenerational Effects - p. 585 64. Chapter 35. Genomic Instability and the Spectrum of Response to Low Radiation Doses - p. 601 65. Chapter 36. Transgenerational Genome Instability in Plants - p. 615 66. Chapter 37. Methods for the Detection of DNA Damage - p. 635 67. Chapter 38. Conserved and Divergent Features of DNA Repair: Future Perspectives in Genome Instability Research - p. 651 68. Index - p. 667
Every species has to preserve the integrity of its genome to ensure faithful passage of genetic information to the progeny. At the same time, there are times during the life of the organism and population in general when a fine balance in genome stability and diversification has to be made to benefit the survival of the species. Genome Stability teaches the reader how various species maintain this fine balance in genome stability and genome diversification in response to their environments.
Genome Stability covers a wide range of topics, including the genome stability of DNA/RNA viruses, prokaryotes, single cell eukaryotes, lower multicellular eukaryotes and mammals. Topics also include major DNA repair mechanisms, the role of chromatin in genome stability, human diseases associated with genome instability as well as changes in genome stability in response to aging. Finally, Genome Stability covers how epigenetic factors contribute to genome stability and how the species pass the memory of the encounters to the progeny, thus influencing the genome of the progeny in an indirect manner. This volume is an essential resource for geneticists, epigeneticists, and molecular biologists who are looking to gain a deeper understanding of this rapidly-expanding field, and can also be of great use to advanced students who are looking to gain additional expertise in genome stability.
1. Introduction - p. xix 2. Chapter 1. Genome Stability: An Evolutionary Perspective - p. 1 3. Section I. Genome Instability of Viruses - p. 18 4. Chapter 2. Genetic Instability of RNA Viruses - p. 21 5. Chapter 3. Genome Instability in DNA Viruses - p. 37 6. Section II. Genome Instability in Bacteria and Archaea - p. 47 7. Chapter 4. Genome Instability in Bacteria and Archaea: Strategies for Maintaining Genome Stability - p. 51 8. Chapter 5. Genome Instability in Bacteria: Causes and Consequences - p. 69 9. Chapter 6. CRISPR: Bacteria Immune System - p. 87 10. Section III. Genome Stability of Unicellular Eukaryotes - p. 98 11. Chapter 7. From Micronucleus to Macronucleus: Programmed DNA Rearrangement Processes in Ciliates Are Regulated Epigenetically by Small and Long Noncoding RNA Molecules - p. 101 12. Chapter 8. Homologous Recombination and Nonhomologous End-Joining Repair in Yeast - p. 117 13. Section IV. Genome Stability in Multicellular Eukaryotes - p. 135 14. Chapter 9. Meiotic and Mitotic Recombination: First in Flies - p. 139 15. Chapter 10. Genome Stability in Drosophila: Mismatch Repair and Genome Stability - p. 155 16. Chapter 11. Genome Stability in Caenorhabditis elegans - p. 163 17. 1. Introduction - p. 163 18. 2. The Caenorhabditis elegans Model - p. 164 19. 3. Powerful Genetic Tools to Explore DDR Dynamics - p. 164 20. 4. Genotoxic Agents for DNA Damage Induction - p. 166 21. 5. Methods for DNA Damage Detection - p. 166 22. 6. Excision Repair - p. 167 23. 7. Mismatch Repair - p. 170 24. 8. Double-Strand Break Repair in C. elegans - p. 170 25. 9. DNA-Damage Checkpoints - p. 175 26. 10. Concluding Remarks - p. 177 27. Glossary - p. 177 28. List of Abbreviations - p. 179 29. Chapter 12. Genetic Engineering of Plants Using Zn Fingers, TALENs, and CRISPRs - p. 187 30. Chapter 13. Plant Genome Stability: General Mechanisms - p. 203 31. Section V. Genome Stability in Mammals - p. 223 32. Chapter 14. Cell-Cycle Control and DNA-Damage Signaling in Mammals - p. 227 33. Chapter 15. The Role of p53/p21/p16 in DNA-Damage Signaling and DNA Repair - p. 243 34. Chapter 16. Roles of RAD18 in DNA Replication and Postreplication Repair - p. 257 35. Chapter 17. Base Excision Repair and Nucleotide Excision Repair - p. 275 36. 1. General Overview and Historical Perspectives of Two DNA Excision-Repair Pathways, BER and NER - p. 275 37. 2. Mammalian BER - p. 276 38. 3. Mammalian NER - p. 283 39. 4. Biological Implications Beyond DNA Damage and Repair - p. 291 40. 5. Interplay Between NER and BER: The Key Role of the DNA-Damage Response for Prevention of Cellular Degeneration - p. 291 41. 6. Concluding Remarks - p. 293 42. Glossary - p. 293 43. List of Abbreviations - p. 294 44. Chapter 18. DNA Mismatch Repair in Mammals - p. 303 45. Chapter 19. Repair of Double-Strand Breaks by Nonhomologous End Joining: Its Components and Their Function - p. 321 46. Chapter 20. Double-Strand Break Repair: Homologous Recombination in Mammalian Cells - p. 337 47. Chapter 21. Telomere Maintenance and Genome Stability - p. 353 48. Chapter 22. The Relationship Between Checkpoint Adaptation and Mitotic Catastrophe in Genomic Changes in Cancer Cells - p. 373 49. Chapter 23. Chromatin, Nuclear Organization, and Genome Stability in Mammals - p. 391 50. Chapter 24. Role of DNA Methylation in Genome Stability - p. 409 51. Chapter 25. Noncoding RNAs in Genome Integrity - p. 425 52. Section VI. Human Diseases Associated With Genome Instability - p. 443 53. Chapter 26. Human Diseases Associated With Genome Instability - p. 447 54. Chapter 27. Cancer and Genomic Instability - p. 463 55. Chapter 28. Chromatin Modifications in DNA Repair and Cancer - p. 487 56. Chapter 29. Genomic Instability and Aging: Causes and Consequences - p. 511 57. Chapter 30. Nucleolar Contributions to DNA-Damage Response and Genomic (In)Stability in the Nervous System - p. 527 58. Section VII. Effect of Environment on Genome Stability - p. 539 59. Chapter 31. Diet and Nutrition - p. 543 60. Chapter 32. Chemical Carcinogens and Their Effect on Genome and Epigenome Stability - p. 555 61. Chapter 33. Environmental Sources of Ionizing Radiation and Their Health Consequences - p. 569 62. Section VIII. Bystander and Transgenerational Effects – Epigenetic Perspective - p. 581 63. Chapter 34. Sins of Fathers Through a Scientific Lens: Transgenerational Effects - p. 585 64. Chapter 35. Genomic Instability and the Spectrum of Response to Low Radiation Doses - p. 601 65. Chapter 36. Transgenerational Genome Instability in Plants - p. 615 66. Chapter 37. Methods for the Detection of DNA Damage - p. 635 67. Chapter 38. Conserved and Divergent Features of DNA Repair: Future Perspectives in Genome Instability Research - p. 651 68. Index - p. 667
