Nasheuer Genome Stability and Human Diseases

1. Auflage 2009
ISBN: 978-90-481-3471-7
Verlag: Springer Netherlands
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 50, 340 Seiten

Reihe: Subcellular Biochemistry

Since the establishment of the DNA structure researchers have been highly interested in the molecular basis of the inheritance of genes and of genetic disorders. Scientific investigations of the last two decades have shown that, in addition to oncogenic viruses and signalling pathways alterations, genomic instability is important in the development of cancer. This view is supported by the findings that aneuploidy, which results from chromosome instability, is one of the hallmarks of cancer cells. Chromosomal instability also underpins our fundamental principles of understanding tumourigenesis: It thought that cancer arises from the sequential acquisition of genetic alterations in specific genes. In this hypothesis, these rare genetic events represent rate-limiting ‘bottlenecks’ in the clonal evolution of a cancer, and pre-cancerous cells can evolve into neoplastic cells through the acquisition of somatic mutations.

This book is written by international leading scientists in the field of genome stability. Chapters are devoted to genome stability and anti-cancer drug targets, histone modifications, chromatin factors, DNA repair, apoptosis and many other key areas of research. The chapters give insights into the newest development of the genome stability and human diseases and bring the current understanding of the mechanisms leading to chromosome instability and their potential for clinical impact to the reader.

Autoren/Hrsg.

Nasheuer, Heinz-Peter

Inhaltsverzeichnis

1;Preface;6
1.1;References;7
2;Contents;8
3;Contributors;10
4;Coming Full Circle: Cyclin-Dependent Kinases as Anti-cancer Drug Targets;13
4.1; Introduction;14
4.2; Overview of Cell Cycle Control in Metazoans and Yeast;15
4.3; Cdk2 Becomes Dispensable;17
4.4; Whats Wrong with This Picture?;19
4.5; Closer to the Mark: Insights into CDK Function from Chemical Genetics;19
4.6; Cdk2 Back in the Saddle?;21
4.7; Conclusions and Perspectives;23
4.8;References;24
5;Core and Linker Histone Modifications Involved in the DNA Damage Response;28
5.1; Introduction;30
5.2; Histone Modifications;31
5.3; Mechanism of Action;32
5.4; Histone Modifications in DNA Repair;33
5.5; Core Histone Modifications in the Repair of DSBs;35
5.5.1; Phosphorylation of H2AX at S139;35
5.5.2; Phosphorylation of H2AX at Y142;36
5.5.3; Methylation of H3K79;38
5.5.4; Methylation of H4K20;39
5.5.5; Methylation of H3K9;39
5.5.6; Ubiquitylation of H2A and H2B;40
5.5.7; Acetylation of Histone H2AX;41
5.5.8; Acetylation of Histone H4;41
5.5.9; Acetylation of Histone H3;42
5.6; The Modification of Linker Histones During DNA Repair;43
5.7; Model for Integrated Role of Histone Modifications in Repair of DSBs;45
5.8; Aberrant Histone Modifications Cause Genome Instability and Disease;46
5.9; Histone Modifying Enzymes and Cancer;47
5.10;References;48
6;Chromatin Assembly and Signalling the End of DNA Repair Requires Acetylation of Histone H3 on Lysine 56;54
6.1; Introduction;55
6.2; Histone Acetylation in the DDR;56
6.3; H3K56ac in the DDR;58
6.4; H3K56ac in Human Cells;60
6.5; Conclusion;63
6.6;References;64
7;Structure and Function of Histone H2AX;66
7.1; Introduction;67
7.1.1; Chromatin Structure and Genome Stability;67
7.1.2; H2AX and DNA Repair;68
7.2; Structural Properties of H2AX;68
7.2.1; Definition of H2AX;69
7.2.2; H2AX Gene;70
7.2.3; H2AX Transcripts;72
7.2.4; H2AX Protein;72
7.2.5; H2AX Post-translational Modifications;75
7.2.6; H2AX Distribution in Chromatin;77
7.2.6.1; Combinatorial Potential in H2AX Distribution;77
7.2.6.2; Simulation of Random H2AX Inclusion;78
7.2.6.3; Functional Implications of H2AX Distribution;80
7.2.6.4; Possibility of Non-random H2AX Distribution;80
7.3; Functional Roles of H2AX;80
7.3.1; Initiation of H2AX Phosphorylation as a Reporter of DSB Events;81
7.3.2; Spreading of H2AX Phosphorylation as a Damage Signal Amplifier;81
7.3.3; H2AX and Chromatin Structural Remodelling;82
7.3.4; H2AX and Localisation of DSB Repair Proteins;83
7.3.5; H2AX and Maintenance of Proximity of Break Ends;84
7.3.6; H2AX and Complementary Damage Signalling via Ubiquitylation;85
7.4; Conclusion;85
7.5;References;85
8;The Initiation Step of Eukaryotic DNA Replication;90
8.1; Introduction ;91
8.2; The Regulators of DNA Replication Initiation;92
8.2.1; Dpb11, Cut5 and TopBP1;92
8.2.2; Sld2 -- A New Player in the Initiation of DNA Replication;93
8.2.3; Sld3-- The Initiator of Initiation;94
8.3; The Replication Factor Cdc45;96
8.3.1; Discovery and Characterization of Cdc45;96
8.3.2; Expression of Cdc45 and Its Control;96
8.3.3; Dynamics of Cdc45 in the Cell;98
8.3.4; Interaction Partners of Cdc45;98
8.3.5; The Role of Cdc45 During DNA Replication;99
8.4; A Phosphorylation Switch for the Initiation of DNA Replication;99
8.5; GINS: An Evolutionarily Conserved Key Playerin DNA Replication;100
8.5.1; Identification of the GINS Complex;100
8.5.2; The Archaeal GINS Complex;102
8.5.3; Structural Studies on the GINS Complex;103
8.5.4; GINS in the Initiation and Elongation Phases of DNA Replication;105
8.6; Initiation and Checkpoint;107
8.6.1; A Role for Initiation Factors During Checkpoint Response;107
8.6.2; DNA Initiation Factors and Stalled DNA Replication Forks;108
8.7; Conclusions;108
8.8;References;109
9;Non-coding RNAs: New Players in the Field of Eukaryotic DNA Replication;116
9.1; Introduction ;117
9.2; Non-coding RNAs in Eukaryotic DNA Replication;118
9.2.1; Y RNA;118
9.2.2; 26T RNA;121
9.2.3; Structured G-Rich RNA;123
9.3; Conclusions;124
9.4;References;126
10;Function of TopBP1 in Genome Stability;130
10.1; Introduction;130
10.2; Role of TopBP1 in DNA Damage Signaling;132
10.2.1; Identification of TopBP1 as a Damage Response Protein;132
10.2.2; Involvement of ATM/ATR in TopBP1 Mediated Damage Response;132
10.2.3; Activation of ATR by TopBP1;134
10.2.4; Implications of TopBP1 in Response to DNA Double-Strand Breaks;136
10.2.5; ADP-Ribosylation of TopBP1;137
10.2.6; Regulation of TopBP1 Activity;137
10.3; TopBP1 in DNA Replication;139
10.4; A Role of TopBP1 During Mitosis and Meiosis;140
10.5; TopBP1 and Regulation of Transcription;141
10.5.1; Regulation of E2F1;141
10.5.2; SPBP and Ets1 Activation;142
10.5.3; Miz1 and UV Damage Response;143
10.5.4; Interaction with c-Abl;144
10.5.5; Hpv16 E2;144
10.5.6; Regulation of TopBP1 Gene Expression;145
10.6; TopBP1 and Cancer;145
10.7; Conclusions;146
10.8;References;147
11;Eukaryotic Single-Stranded DNA Binding Proteins: Central Factors in Genome Stability;153
11.1; General Overview;154
11.2; Replication Protein A;155
11.2.1; Physical Interactions of RPA with DNA;157
11.2.2; The RPA Complex and Its Binding to Proteins;159
11.2.2.1; The RPA Complex and DNA Replication;159
11.2.2.2; The RPA Complex in DNA Repair Processes -- Molecular Counting Capabilities;161
11.2.3; RPA Phosphorylation;163
11.2.4; An Alternative Form of Replication Protein A;164
11.2.5; Replication Protein A -- The Cancer Link;164
11.3; The Human ssDNA-Binding Protein hSSB1;165
11.4; Mitochondrial SSBs;166
11.4.1; Human mtSSB and p53;166
11.5;References;167
12;DNA Polymerases and Mutagenesis in Human Cancers;174
12.1; Genome Stability Control Mechanisms and the Replication Fork;174
12.2; DNA Repair and Mutagenesis;178
12.3; DNA Polymerases and Mutagenesis;184
12.3.1; Replicative Pols;184
12.3.2; DNA Repair Pols;185
12.3.3; TLS Pols;186
12.4; Concluding Remarks;189
12.5;References;190
13;DNA Polymerase , a Key Protein in Translesion Synthesis in Human Cells;198
13.1; Introduction;199
13.2; DNA Polymerase , a Member of the Y Family of Polymerases;200
13.3; Role of Pol in Bypass of Lesions Induced by Platinum-Based Chemotherapeutic Drugs;202
13.4; Role of Pol in Bypass of Other Lesions in DNA;204
13.5; Regulation of Pol Recruitment;204
13.6; Activation of DNA Damage Responses in Pol -Deficient Cells;207
13.7; Regulation of Pol Expression;209
13.8; Concluding Remarks;210
13.9;References;211
14;The Mitochondrial DNA Polymerase in Health and Disease;219
14.1; Introduction;219
14.2; Pol in mtDNA Replication;220
14.3; Pol in Mitochondrial DNA Repair;222
14.4; Mitochondrial Toxicity from Antiviral Inhibition of Pol ;222
14.5; Disease Mutations in the POLG Gene;224
14.6;References;227
15;Centromeres: Assembling and Propagating Epigenetic Function;231
15.1; Introduction;232
15.2; Specifying the Centromere;233
15.2.1; Centromeric DNA;233
15.2.2; Evidence for Epigenetic Behavior at the Centromere;234
15.3; Chromatin and Centromere Determination;234
15.3.1; CENP-A, The Centromere Specific Histone;235
15.3.2; CENP-A Nucleosomes;236
15.3.3; Organization of CENP-A Within Centromeres;236
15.4; Assembly of CENP-A Chromatin and the Constitutive Centromere-Associated Network of Proteins;238
15.4.1; CENP-A Assembly in the Cell Cycle;238
15.4.2; Heritability and Dynamics of Centromeric Chromatin Proteins;239
15.4.3; Targeting CENP-A to the Centromere;240
15.4.4; Assembly of the Constitutive Centromere-Associated Network, CCAN;242
15.5; Kinetochore Function, Assembly and Signaling in the Spindle Assembly Checkpoint;245
15.5.1; Kinetochore Structure and Function;246
15.5.2; The Core Microtubule-Attachment Site -- KMN Network;247
15.5.3; Controlling Dynamics of Kinetochore-Microtubule Attachment and Chromosome Movement;247
15.5.4; Spindle Assembly Checkpoint (SAC): Maintaining Fidelity of Chromosome Segregation;248
15.6; Summary;250
15.7;References;251
16;Nucleotide Excision Repair in Higher Eukaryotes: Mechanism of Primary Damage Recognition in Global Genome Repair;258
16.1; Introduction;259
16.2; The Order of Protein Assembly in GG-NER;260
16.3; Advantages of Sequential Assembly of the Repair Complex;262
16.3.1; Models of DNA Damage Recognition;262
16.3.2; XPC-hHR23B Complex as a Potential Sensor of Helix Distortion;265
16.3.3; Role of UV-DDB in DNA Damage Recognition;266
16.3.4; Roles of XPA and RPA in NER;267
16.4; Photoreactive DNA Intermediates as a Tool to Study NER Assembly;269
16.4.1; Verification of Photoreactive dNMP Analogues as NER Substrates;269
16.4.2; Crosslinking of XPC-hHR23B to Photoreactive DNA is Moderated by XPA and RPA;272
16.4.3; Undamaged Strands are Strongly Required for XPC-hHR23B Crosslinking to Damaged DNA Duplexes;273
16.4.4; Localization of NER Factors on Undamaged Strand of Damaged DNA Duplex;275
16.5;References;278
17;Nonhomologous DNA End Joining (NHEJ) and Chromosomal Translocations in Humans;285
17.1; Frequency and Causes of Double-Strand Breaks;287
17.2; Vertebrate Nonhomologous DNA End Joining;288
17.2.1; The DNA Ligase IV Complex;289
17.2.2; The DNA Polymerases of NHEJ;290
17.2.3; Artemis, DNA-PKcs and the Nuclease of NHEJ;291
17.2.4; Concluding Comments on Vertebrate NHEJ;292
17.3; Chromosomal Translocations;292
17.3.1; Types of Translocations and Relation to Cancer;292
17.3.2; NHEJ in Chromosomal Structural Changes;293
17.3.3; Causes of DSBs That Initiate Translocations;293
17.3.3.1; Mistakes of V(D)J Recombination;295
17.3.3.2; Sequential Action by AID and the RAG Complex;295
17.3.3.3; Source of Single-Strandedness at Sites where AID Acts on meC Sites;298
17.3.3.4; Concluding Comments;298
17.3.4;References;299
18;Fluorescence-Based Quantification of Pathway-Specific DNA Double-Strand Break Repair Activities: A Powerful Method for the Analysis of Genome Destabilizing Mechanisms;303
18.1; Background;303
18.1.1; Implications of Pathway-Specific DNA Double-Strand Break Repair Activities;303
18.1.2; Fluorescence-Based DSB Repair Analysis;305
18.2; Materials;307
18.2.1; Solutions and Reagents;307
18.2.2; Equipment;308
18.2.3; Protocols;308
18.2.3.1; Transfection of MEFs with Repair Assay Plasmids;308
18.2.3.2; Co-transfection of MEFs with siRNA and Repair Assay Plasmids;309
18.2.3.3; Processing of Cells for Flow Cytometric Quantification of EGFP-Positive Cells;309
18.2.3.4; Processing Cells for Cell Cycle Analysis in 96-Well Plate;310
18.2.3.5; General Notes;311
18.2.4;References;311
19;Apoptosis: A Way to Maintain Healthy Individuals;313
19.1; Introduction;314
19.2; Apoptosis: General Considerations;314
19.3; Apoptosis During Embryogenesis and Development;316
19.3.1; Developmental Apoptosis and Model Organisms;316
19.3.2; Apoptosis and Germ Cells;317
19.3.3; Apoptosis in Neurons and Lymphocytes;318
19.4; Apoptosis and DNA Damage;319
19.4.1; Apoptosis Regulators in Response to DNA Damage;319
19.4.2; Apoptosis and Aneuploidy;320
19.5; Concluding Remarks;323
19.6;References;324
20;The Use of Transgenic Mice in Cancer and Genome StabilityResearch;330
20.1; Introduction;331
20.2; Evolution of Mouse Models of Cancer;332
20.2.1; Spontaneous and Carcinogen-Induced Cancers in Mice;332
20.2.2; Xenograft Models;332
20.2.3; Transgenic Mice;333
20.3; Production of Transgenic Mice;333
20.3.1; Pronuclear Injection;333
20.3.2; Genetically Engineered Mouse Embryonic Stem Cells;334
20.4; Types of Transgenic Mice;334
20.4.1; Traditional Transgenic Mouse Models;334
20.4.2; Conditional Transgenic Mouse Models;336
20.5; Uses of Transgenic Mice in Cancer Research;336
20.5.1; Mouse Models of Metastasis and Tissue Invasion;336
20.5.2; Mouse Models of Angiogenesis;337
20.5.3; Transgenic Mice Models in the Development of Cancer Therapeutics;337
20.6; Uses of Transgenic Mice in Genome Stability Research;338
20.7; Outlook;339
20.8;References;340
21;Index;342