Front Cover 1
Title Page 4
Copyright Page 5
Table of Contents 6
Contributors 10
Preface 16
PART I Overview 18
Chapter 1 Overview of the Field 20
I. Introduction 20
II. The Current Spectrum of Expanded Repeats in Human Diseases 21
III. Instability of Microsatellite Repeats 21
A. Repeat Instability in Patient-Derived Tissues 24
B. Molecular Mechanisms of Genetic Instability 24
C. Microsatellite Repeat Instability and Population Genetics 28
IV. Pathogenic Mechanism of Neurological Diseases Caused by Expanded Microsatellites Repeats 28
A. Genotype\u2013Phenotype Correlation 28
B. Pathogenic Mechanisms 29
V. Future Directions for Research on Repeats and Genomic Instabilities in Neurological Disorders 30
VI. Concluding Remarks 31
References 31
PART II Myotonic Dystrophy 36
Chapter 2 Myotonic Dystrophies: An Overview 38
I. Introduction 38
II. Clinical Phenotype 39
A. Multisystemic Phenotype 39
B. Anticipation 41
C. Congenital Myotonic Dystrophy 41
III. The Mutation Responsible for Myotonic Dystrophies 41
A. Mapping and Identification of the DM1 and DM2 Mutations 41
B. Molecular Explanations for Anticipation, Congenital Myotonic Dystrophy, and Parental Gender Effects 42
C. Instability of (CTG)n and (CCTG)n Repeats in Myotonic Dystrophies 42
IV. Pathogenic Mechanisms of Myotonic Dystrophies 45
A. Pathogenic Mechanism of DM1 45
B. Molecular Pathogenesis of DM2 46
C. Molecular Basis of Phenotypic Differences between DM1 and DM2 46
V. Impact of Advanced Knowledge in Myotonic Dystrophy on Diagnostics and Therapeutics 46
VI. Concluding Remarks 47
Acknowledgment 47
References 47
Chapter 3 The RNA-Mediated Disease Process in Myotonic Dystrophy 54
I. Introduction 54
II. Evidence for an RNA-Mediated Disease Mechanism in DM1 55
A. Evidence against Conventional Mechanisms for Genetic Dominance 55
B. Evidence for the RNA-Dominant Genetic Mechanism 56
C. Effects of Expanded Poly(CUG) on Intracellular Transcript Localization 57
D. Cell Culture Models of DM1 Involving Overexpression of CUG Expansion RNA 57
E. Transgenic Mouse Models of DM1 Involving Overexpression of CUG Expansion RNA 57
F. DM2 Results from Expression of Untranslated CCUG Repeats 59
III. Biochemical Basis for RNA-Mediated Disease 59
A. Mutant DMPK and ZNF9 RNAs Are Retained in the Nucleus 59
B. Alternative Splicing of Pre-mRNAs 60
C. Alternative Splicing Is Disrupted in DM 61
D. Mechanisms for Misregulated Alternative Splicing: Role for CELF and MBNL Proteins 63
E. CELF Proteins Are RNA Splicing Regulators 64
F. Muscleblind Sequestration Model for DM 65
IV. Unanswered Questions for the RNA-Mediated Disease Process in DM 67
A. What Is the Molecular Basis for the Postnatal Splicing Switch Affected in DM? 67
B. Are Other Biochemical Pathways Altered in DM? 67
C. Why Do Existing Mouse Models Fail to Recapitulate Congenital DM Phenotypes? 67
References 67
Chapter 4 cis Effects of CTG Expansion in Myotonic Dystrophy Type 1 72
I. Introduction 73
II. Myotonic Dystrophy Type 1 73
A. Genetics of DM1 73
B. Mechanism of CTG Repeat Instability 74
C. Age at Onset and Disease Course of DM1 74
D. Clinical Features of DM1 74
III. Myotonic Dystrophy Type 2 76
A. Genetics of DM2 76
B. Age at Onset and Disease Course in DM2 76
C. Clinical Features of DM2 76
IV. What Do the Genetics of DM1 and DM2 Tell Us about the Etiology of These Disorders? 78
V. Dominant RNA Effects Contribute to DM1 Skeletal Muscle Disease 78
VI. What Is the Mechanistic Basis of the Toxicity Associated with CUG Repeat Expression? 78
VII. Proteins That Interact with CUG Repeat Sequences 79
VIII. Is the Toxicity of CUG/CCUG Different? 80
IX. cis Effects of CTG Expansion at the DM1 Locus 80
X. Role of Decreased DMPK Levels in the Etiology of DM1 81
A. DMPK 81
B. Targeted Inactivation of Dmpk in Mice 82
C. Loss of Dmpk Does Not Result in Gonadal Dysfunction, Cataracts, or Features of Congenital DM1 82
D. Loss of Dmpk Results in Decreased Twitch and Tetanic Force Development in the Sternomastoid 82
E. Depolarization-Mediated Calcium Efflux from the Sarcoplasmic Reticulum Is tilde 40% Smaller in Dmpk-/- Myotubes 83
F. Dmpk-Deficient Mice Have Altered Sodium Channel Gating, with Reopenings Leading to Persistent Depolarizing Current in Skeletal Muscle 84
G. Dmpk Deficiency May Contribute to Skeletal Muscle Weakness and Myotonia in DM1 84
H. Inactivation of Dmpk Results in Cardiac Conduction Disorders 85
I. Dmpk-Deficient Mice Have Altered Sodium Channel Gating in Cardiac Muscle 86
J. Dmpk-Deficient Mice Show Decreased Phosphorylation of Phospholamban 86
K. Dmpk Loss Alters Hippocampal Function 87
XI. Role of Decreased SIX5 Levels in the Etiology of DM1 87
A. SIX5 87
B. Targeted Deletion of Six5 Sequences in Mice 87
C. Decreased Six5 Levels Do Not Result in Skeletal Muscle Defects 88
D. Decreased Six5 Levels Result in Infrahisian Conduction Disease and Ventricular Hypertrophy 88
E. Six5 Deficiency Results in Nuclear Cataracts 89
F. Six5 Loss Results in Elevated FSH Levels,Testicular Atrophy, Leydig Cell Hyperproliferation, and Aberrant Spermiogenesis 89
XII. Possible Contribution of Other cis Effects at the DM1 Locus 91
XIII. Concluding Remarks 91
References 92
Chapter 5 Normal and Pathophysiological Significance of Myotonic Dystrophy Protein Kinase 96
I. Introduction 97
II. Myotonic Dystrophy Protein Kinase 98
A. Tissue Expression and in Situ Localization 98
B. Alternative Splicing 99
C. AGC Serine/Threonine Protein Kinase Group 101
III. The Role of Individual Protein Domains 101
A. N-Terminal Leucine-Rich Domain 101
B. Serine/Threonine Protein Kinase Domain 103
C. VSGGG Motif 104
D. Coiled-Coil Region 104
E. C-Terminal Tails 105
IV. Substrates and Function 106
A. DMPK and Ion Homeostasis 106
B. DMPK and the Actomyosin Cytoskeleton 108
C. SRF, CUG-BP, and MKBP 108
V. Transgenic Mice 109
A. DMPK Knockout Mice 109
B. Tg26-hDMPK 109
VI. Concluding Remarks 109
Acknowledgments 110
References 110
Chapter 6 Biochemistry of Myotonic Dystrophy Protein Kinase 116
I. Introduction 116
II. Structure of Dm-1 Locus and Region 117
III. DMPK Structural Domains 117
A. Leucine-Rich Repeat: Amino-Terminal Region 117
B. Catalytic Domain 118
C. Carboxy-Terminal Region 118
D. Coiled-Coil Region 118
IV. Alternative Splicing and DMPK Isoforms 118
V. Functional Biochemical Properties of DMPK 118
A. Homodimerization through the Coiled-Coil Region 119
B. Interaction with Other Regulatory Proteins 119
C. Substrate Specificity 119
VI. DMPK Family of Protein Kinases 120
VII. Tissue Expression of DMPK 121
A. Heart 121
B. Lens 121
C. Skeletal Muscle 121
D. Brain 122
VIII. Subcellular Localization of DMPK 122
A. Carboxy-Terminal Membrane Anchoring 123
B. Endoplasmic Reticulum, Mitochondrial, and Cytosolic Localization 123
IX. DMPK Function in Heart and Brain 123
A. Excitability of Heart 123
B. Synaptic Plasticity in Brain 123
X. Multiple Mechanisms in Dm-1 Pathogenesis 125
A. Effects of Local Chromatin Perturbation on the Expression of Neighboring Genes and DMPK 125
B. Perturbation of Alternative RNA Splicing 125
C. Haploinsufficiency of DMPK 126
XI. Conclusion 126
Acknowledgments 126
References 126
Chapter 7 Clinical and Genetic Features of Myotonic Dystrophy Type 2 132
I. Introduction 132
II. Genetic Features of DM2 133
A. History 133
B. DM2 Gene Identification 133
C. Haplotype Analysis and Conservation 133
D. Somatic Mosaicism 134
E. Diagnostic Methods 134
F. Intergenerational Changes 137
G. Genotype\u2013Phenotype Correlation 138
III. Clinical Features of Myotonic Dystrophy 139
A. Muscle Pathology 139
B. Multisystemic Features 139
C. Central Nervous System Involvement 140
IV. Pathophysiological Models 140
A. DM Pathogenic Models prior to DM2 140
B. Identification of DM2 Indicates Breadth of RNA Effects in DM Pathogenesis 140
C. Gain-of-Function RNA Model 140
V. CUG-BP and Muscleblind 141
A. CUG-BP 141
B. Muscleblind 142
C. Downstream Targets of CUG-BP and Muscleblind 142
VI. Potential Causes of Clinical Distinctions between DM1 and DM2 143
VII. Conclusions 143
References 143
Chapter 8 Myotonic Dystrophy Type 2: Clinical and Genetic Aspects 148
I. Introduction 149
II. Clinical Phenotype 150
A. Symptoms and Findings in DM2 150
B. Age of Onset and Anticipation in DM2 151
C. Homozygosity for DM2 Mutation 152
D. What Is the Full Phenotypic Spectrum of DM2? 152
E. Muscle Biopsy and Morphological Findings 152
III. Molecular Genetics 153
A. Characteristics of the DM2 Repeat 153
B. Evolutionary Conservation of the DM2 Repeat 154
C. Population Studies and the Origin of the DM2 Repeat Expansion 154
D. Molecular Diagnosis of DM2 155
E. How Many Myotonic Dystrophies Are There? 156
IV. Molecular Pathophysiology 159
V. Concluding Remarks 161
Acknowledgments 162
Note Added in Proof 162
References 162
Chapter 9 The Subtelomeric D4Z4 Repeat Instability in Facioscapulohumeral Muscular Dystrophy 168
I. Introduction 168
II. Clinical Characteristics 169
III. Ancillary Investigations 169
IV. Linkage Analysis 169
V. Genetic/Linkage Heterogeneity 171
VI. Genetic Diagnosis of FSHD 171
VII. Timing and Origin of the D4Z4 Rearrangement 172
VIII. Candidate Genes 172
IX. Chromatin Remodeling 173
X. Myoblast Studies 176
XI. Concluding Remarks 176
Acknowledgments 176
References 177
PART III Fragile X Syndrome 180
Chapter 10 Fragile X Syndrome and Fragile X-Associated Tremor/Ataxia Syndrome 182
I. Introduction 182
II. Fragile X Syndrome 183
A. Spectrum of Clinical Involvement 183
B. Clinical Involvement in Premutation Carriers 184
III. Fragile X-Associated Tremor/Ataxia Syndrome 184
A. Overview 184
B. Clinical Features 185
C. Epidemiology 185
D. Neuropathology 187
E. Molecular Pathogenesis 187
IV. Concluding 188
Acknowledgments 188
References 188
Chapter 11 Animal Models of Fragile X Syndrome: Mice and Flies 192
I. Introduction 192
II. Mouse Models 194
A. Fmr 1 Knockout Mice 194
B. Macroorchidism 195
C. Neuroanatomy and Physiology of the Knockout Brain 196
D. Structural Abnormalities 197
E. LTP/LTD 197
F. Behavior 198
G. Environmental Effects 200
H. Instability of the CGG Repeat in Mice 200
I. Mouse Model for FXTAS 201
J. Knockout Mice for Fmr 1 Paralogs Fxr 1 and Fxr 2 201
III. Flies 202
A. Behavioral Phenotypes 204
B. Neuronal Phenotypes 204
C. Modifying Phenotypes with Genes and Drugs 205
D. Biochemistry 206
E. FXTAS and CGG Models 206
IV. Conclusion 207
Acknowledgments 207
References 207
Chapter 12 Chromosomal Fragile Sites: Mechanisms of Cytogenetic Expression and Pathogenic Consequences 212
I. Introduction 212
II. Historical Aspects of Chromosomal Fragile Sites 213
III. \u201cRare\u201d Fragile Sites 213
A. Folate-Sensitive Rare Fragile Sites 213
B. Nonfolate-Sensitive Rare Fragile Sites 214
IV. \u201cCommon\u201d or Constitutive Fragile Sites 214
A. Mechanism of Cytogenetic Formation 214
B. Contribution to Cancer 217
V. Conclusions 220
Acknowledgments 220
References 220
PART IV Kennedy\u2019s Disease 226
Chapter 13 Clinical Features and Molecular Biology of Kennedy\u2019s Disease 228
I. Introduction 228
II. Clinical Features of SBMA 229
III. Laboratory Studies 229
IV. Differential Diagnosis 229
V. Management 230
VI. Genetics of SBMA 230
VII. The Androgen Receptor 230
A. Structure of the Androgen Receptor Gene and Protein 230
B. Androgen Receptor Activat 230
C. The Androgen Receptor Ligands 231
VIII. Androgen Receptor Function in the Nervous System 231
IX. Pathological Mechanisms in SBMA 232
A. Toxic Gain of Function 232
B. Inclusions and Aggregates 232
C. Ligand-Dependent Effects in SBMA Models 233
X. Therapeutic Approaches in SBMA 234
A. Histone Deacetylase Inhibitors 234
B. Anti-androgens 234
References 234
PART V Huntington\u2019s Disease 238
Chapter 14 Molecular Pathogenesis and Therapeutic Targets in Huntington\u2019s Disease 240
I. Introduction 240
II. Mechanisms of HD Pathogenesis 241
A. Mutant Huntingtin Aggregation and InclusionBody Formation 241
B. Toxicity of Huntingtin N-Terminal Fragments 242
C. Cellular Protein Quality Control Mechanisms 243
D. The Autophagy\u2013Lysosome Pathway in HD 245
E. Impairment of Axonal Transport 246
F. Transcriptional Dysregulation 246
III. Experimental Therapeutics in Models of HD 247
A. Models Used for Identification of Potential Therapeutic Agents 248
B. Preclinical Testing in Mouse Models of HD 252
IV. Conclusion 259
Acknowledgments 259
References 259
Chapter 15 Molecular Pathogenesis of Huntington\u2019s Disease:The Role of Excitotoxicity 268
I. Introduction 268
II. Glutamate and Neurotransmission 268
III. Glutamate and Excitotoxicity 269
A. NMDA Receptors Play a Key Role in Calcium-Induced Excitotoxicity 269
B. Disruption of Calcium Signaling Activates Neurotoxic Processes 270
C. Role of the Mitochondria 270
IV. Excitotoxicity and HD 271
A. NMDA Recept 271
B. mGluR5 and InsP3R1 Receptors 272
C. Mitochondria 273
V. Implications for Therapy 273
VI. Concluding Remarks 275
Acknowledgments 275
References 275
Chapter 16 Huntington\u2019s Disease-like 2 278
I. Introduction 278
II. Detection of the HDL2 Expansion Mutation 280
III. HDL2 at the Bedside 280
IV. HDL2 and Neuroacanthocytes 280
V. Neuropathology of HDL2 281
VI. Epidemiology of HDL2 281
VII. JPH3 and HDL2: Phenotype\u2013Genotype Relationship 282
VIII. HDL2 Is Not a Polyglutamine Disease 283
IX. The HDL2 Locus and Junctophilin-3: Structure and Function 283
X. HDL2 and Toxic Transcripts 286
XI. HDL2 and Intranuclear Protein Aggregates 286
XII. Conclusion 287
Acknowledgments 287
References 287
PART VI Friedreich\u2019s Ataxia 292
Chapter 17 Friedreich\u2019s Ataxia 294
I. Introduction 294
II. Clinical and Pathological Aspects of Friedreich\u2019s Ataxia 295
A. Epidemiology 295
B. Pathology 296
C. Clinical Aspects 297
D. Prognosis 300
III. Isolation and Analysis of the Friedreich Ataxia Gene 301
A. Mapping and Cloning of the FRDA Gene 301
B. Structure of the FRDA Gene 301
C. Expression of the FRDA Gene 301
IV. Gene Mutations in FRDA 302
A. Point Mutations 302
B. GAA Trinucleotide Repeat Expansion 302
C. Detection and Diagnostic Value of Expanded GAA Repeats 303
D. Instability of the Expanded GAA Triplet Repeat 304
V. Origin of the Expanded GAA Repeat 304
VI. Pathogenic Mechanism of the GAA Expansion 305
A. Effect of the Expanded GAA Repeat on Frataxin Gene Expression 305
B. Properties of the Expanded GAA Repeat 306
VII. Phenotype\u2013Genotype Correlation 307
VIII. Conclusion and Perspectives 308
References 308
Chapter 18 Experimental Therapeutics for Friedreich\u2019s Ataxia 314
I. Introduction 314
II. Parabenzoquinones 315
A. Rationale 315
B. Idebenone 315
C. Coenzyme Q10 317
D. MitoQ 318
E. EPI-A0001 318
III. Selenium and Glutathione Peroxidase Mimetics 318
IV. Creatine and Carnitine 318
V. FRDA Upregulation 318
VI. Summary 319
References 319
Chapter 19 Evolution and Instability of the GAA Triplet-Repeat Sequence in Friedreich\u2019s Ataxia 322
I. Introduction 323
II. Origin and Evolution of Polymorphic GAA-TR Alleles at the FXN Locus 323
III. Geographic Distribution and Population Genetics of the GAA-TR Mutation 326
IV. Intergenerational Instability of GAA-TR Alleles at the FXN Locus 328
V. Somatic Instability of GAA-TR Alleles at the FXN Locus 329
VI. Is the GAA-TR Sequence at the FXN Locus Unique? 333
VII. Concluding Remarks 334
References 334
Chapter 20 Mouse Models for Friedreich\u2019s Ataxia 338
I. Introduction 338
II. Mouse Models for Friedreich\u2019s Ataxia 339
A. Conditional Knockout Models 339
B. Inducible Conditional Knockout Models 340
C. Models that Reproduce the Molecular Defect 341
References 342
Chapter 21 Triplexes, Sticky DNA, and the (GAA cdot TTC) Trinucleotide Repeat Associated withFriedreich\u2019s Ataxia 344
I. Introduction 344
II. DNA Structures Associated with (R cdot Y) Sequences 345
A. Triplexes 345
B. Sticky DNA 346
III. Sticky DNA Properties and Detection 346
A. Requirements for Sticky DNA Formation 346
B. Assays for Detection of Sticky DNA 347
IV. Effect of Sticky DNA on Cellular Mechanisms 349
A. Transcription 349
B. Replication 349
C. Recombination 350
V. Concluding Remarks 350
Acknowledgments 350
References 350
PART VII Spinocerebellar Ataxias 354
Chapter 22 Phosphorylation of Ataxin-1: A Link Between Basic Research and Clinical Application in Spinocerebellar Ataxia Type 1 356
I. Introduction 357
II. Insights into Normal Ataxin-1 Function 357
III. Factors Mediating SCA1 Pathogenesis 358
IV. Phosphorylation of Ataxin-1: A Mediator of SCA1 Pathogenesis 359
A. Phosphorylation Sites in Ataxin-1 359
B. Localization of Phosphorylated S776-Ataxin-1 359
C. S776 and Ataxin-1 Aggregation 359
D. S776 and SCA1 Pathogenesis in Vivo 359
E. 14-3-3: An Ataxin-1 Interactor 361
F. 14-3-3 Stabilizes Ataxin-1 361
G. 14-3-3 and Neurodegeneration in Vivo 361
V. AKT Signaling: A Role in SCA1 Pathogenesis? 361
A. AKT and Ataxin-1 Phosphorylation 361
B. AKT Mediates the 14-3-3/Ataxin-1 Interaction 362
C. AKT-Dependent Ataxin-1 Phosphorylation and SCA1 Pathogenesis 362
D. PI3K/AKT Pathway and SCA1 Pathogenesis 362
VI. The Search for Modifiers of Ataxin-1 S776 Phosphorylation 362
A. Development of a Cell-Based Assay for Ataxin-1 Phosphorylation 362
B. Inhibitors of Ataxin-1 Phosphorylation 363
C. Ataxin-1 Signaling Pathways 363
VII. Concluding Remarks 364
References 364
Chapter 23 Spinocerebellar Ataxia Type 2 368
I. Introduction 368
II. Identification of the SCA2 Gene 368
III. Repeat Range 369
IV. Anticipation and Meiotic Instability of the SCA2 Repeat 369
V. Genetic Modifiers of Age of Disease Onset 370
VI. Frequency and Phenotype 371
A. Ataxia 371
B. Eye Movements and Retinal Changes 371
C. Movement Disorders 372
D. Neuropathy 372
E. Dementia 372
VII. Neuropathology 372
VIII. Function 373
A. Sequence Homologies and Protein Domains 373
B. Expression Patterns 374
C. Function 374
IX. Mouse Models 375
X. Outlook 375
References 375
Chapter 24 Machado\u2013Joseph Disease/Spinocerebellar Ataxia Type 3 380
I. Clinical Features 381
II. Neuropathological Features 382
III. Molecular Genetic Features 382
IV. The MJD1 Gene Product, Ataxin-3 383
V. Protein Misfolding as a Central Feature of Pathogenesis 385
VI. Further Insights from Animal Models 387
VII. Toward Therapy 389
References 389
Chapter 25 Spinocerebellar Ataxia Type 6 396
I. Introduction 396
II. Etiology, Pathogenesis, and Neuropathology 397
III. Clinical Manifestation 398
IV. Examination and Diagnosis 399
V. Treatment, Prognosis, and Perspective 399
References 400
Chapter 26 Pathogenesis of Spinocerebellar Ataxia Type 7: New Insights from Mouse Models and Ataxin-7 Function 404
I. Introduction 404
II. Ataxin-7, the Protein Mutated in SCA7 405
A. Expression Levels and Subcellular Localization 405
B. Ataxin-7 Function 406
C. Ataxin-7 Paralogs 406
D. Ataxin-7 Incorporation into TFTC-Type Complexes Is Not Affected by PolyQ Expansion 407
E. Future Directions: Effect of PolyQ-Expanded ATXN7 on TFTC/STAGA Function 407
III. SCA7 Pathogenesis 407
A. Phenotypic and Neuropathological Abnormalities of SCA7 Mouse Models 407
B. Retinal Pathology of SCA7 Mice 408
C. Aggregation of Mutant Ataxin-7 into Nuclear Inclusions 408
D. Proteolytic Processing of Mutant Ataxin-7 409
E. Polyglutamine Expansion Stabilizes Ataxin-7 409
F. Chaperones and the Ubiquitin\u2013Proteasome System 409
G. Transcriptional Dysregulation in SCA7 Retinal Dysfunction 410
IV. Concluding Remarks 411
Acknowledgments 412
References 412
Chapter 27 Spinocerebellar Ataxia Type 7: Clinical Features to Cellular Pathogenesis 416
I. Introduction 416
II. Neuropathology 418
III. Disease Gene Identification, Size Ranges, and Spectrum of Severity 419
IV. Repeat Instability in SCA7 419
V. SCA7 Neurodegeneration: Models and Mechanisms 421
VI. SCA7 Retinal Degeneration: Identification of Molecular Players and Pathways 424
VII. Ataxin-7 Normal Function Provides Clues to SCA7 Disease Pathogenesis 425
VIII. Ataxin-7 Proteolytic Cleavage and Turnover 427
IX. Unanswered Questions and Future Directions 428
Acknowledgments 429
References 429
Chapter 28 Molecular Genetics of Spinocerebellar Ataxia Type 8 434
I. Introduction 434
II. Identification of the SCA8 CTG Repeat Expansion 435
A. RAPID Cloning 435
B. Organization of the SCA8 Disease Gene 435
III. The CTG Repeat Expansion Cosegregates with a Novel Form of Ataxia 436
A. SCA8 Expansion Screening in Families with Unknown Forms of Ataxia 436
B. Clinical Features of SCA8 436
C. Neuropathology of SCA8 436
IV. Reduced Penetrance Commonly Found in SCA8 438
A. Disease Penetrance in the MN-A Family Is Affected by CTG Length 438
B. Reduced Penetrance in Other Families 438
C. SCA8 Expansions on Control Chromosomes 438
V. Genetic Analysis of SCA8 Expansion Chromosomes 440
A. Haplotype Analysis of SCA8 Expansion Chromosomes 440
B. SCA8 Expansions Cosegregate with Ataxia in Small Families 440
VI. SCA8 Repeat Instability: Possible Influences on Disease Penetrance 442
A. Length of the Polymorphic CTA Repeat Tract Preceding the CTG Expansion 442
B. Duplicating Interruptions within the CTG Expansion 442
C. Repeat Instability during Transmission 443
D. En Masse CTG Repeat Contractions in Sperm 444
E. Germline Instability of the CTG Repeat Expansion by Small Pool PCR 444
VII. Molecular Parallels with Myotonic Dystrophy 445
VIII. Modeling SCA8 Pathogenesis Using the Mouse and Fly 445
IX. Conclusions 446
References 446
Chapter 29 Spinocerebellar Ataxia Type 10: A Disease Caused by an Expanded (ATTCT)n Pentanucleotide Repeat 450
I. Introduction 450
II. Identification and Characterization of the SCA10 Mutation 451
A. Identification of the (ATTCT)n Expansion as the SCA10 Mutation 451
B. Structure of the (ATTCT)n Repeat 453
C. Instability of the Expanded (ATTCT)n Repeat 455
III. Clinical Phenotype and Ethnicity 459
A. Spectrum of the SCA10 Phenotype 459
B. Ethnic Distribution of SCA10 and Phenotypic Variations 459
IV. Genotype\u2013Phenotype Correlation 460
V. Diagnostic Utility of the Mutation 460
VI. Pathogenic Mechanisms 460
A. ATXN10 Gene and Function of the Ataxin-10 Protein 460
B. Pathogenic Models for SCA10 461
VII.Conclusion 462
References 462
Chapter 30 DNA Structures and Genetic Instabilities Associated with Spinocerebellar Ataxia Type 10 (ATTCT)n cdot (AGAAT)n Repeats Suggest a DNA Amplification Model for Repeat Expansion 464
I. Introduction 465
A. DNA Unwinding, Replication, and Transcription 465
B. Eukaryotic DNA Replication and the Promiscuous Replication Hypothesis 466
II. The SCA10 Repeat Forms Unwound DNA 467
III. Complex Replication-Based Instability of SCA10 (ATTCT)n cdot (AGAAT)n Repeats in Escherichia coli 471
A. SCA10 Repeats Do Not Undergo Deletion at a High Rate in Escherichia coli 471
B. Complex Expansion Mutations Occur in (ATTCT)n cdot (AGAAT)n Repeats in Escherichia coli 471
IV. Models for Complex Expansion Mutations in Escherichia coli and Expansion and Instability in Humans 472
A. Mechanisms Leading to the Formation of the Complex Expansion Mutation in Escherichia coli 472
B. Amplification Leading to Repeat Expansion in Human Cells 473
V. Concluding Remarks 473
References 474
Chapter 31 Spinocerebellar Ataxia Type 12 478
I. Introduction 479
II. SCA12 Epidemiology and Genetics 479
III. SCA12 Clinical Aspects 480
A. Clinical Features 480
B. Neuroimaging and Neuropathology 481
C. Diagnostic Considerations 481
IV. Molecular Basis of SCA12 482
A. SCA12 Repeat Lies in the 5' Region of the Most Common PPP2R2B Transcript 482
B. Alternately Spliced PPP2R2B Transcripts Encode Alternate Isoforms of B beta 482
C. SCA12 Is Not a Polyglutamine Disease 484
V. Function of PPP2R2B Gene Products 484
A. Protein Phosphatase 2A 484
B. Expression of B-Family Regulatory Subunits 485
C. Structure of B-Family Regulatory Subunits 486
D. B beta Isoforms Determine Subcellular Localization of PP2A 486
VI. Possible Mechanisms of Disease Pathogenesis 486
References 488
Chapter 32 Spinocerebellar Ataxia 17 and Huntington\u2019s Disease-like 4 492
I. Introduction 492
II. Genetic Aspects of SCA17\u2013HDL4 493
A. Size and Structure of the Normal Repeat 493
B. Behavior of the Pathological Expansions: Range and Incomplete Penetrance 493
C. Instability and Origin of the Expansions 494
D. Epidemiology and Relative Frequency of SCA17 495
III. Phenotype of SCA17\u2013HDL4 495
A. Clinical Heterogeneity 495
B. Phenotype\u2013Genotype Correlations 496
C. Neuropathology of SCA17\u2013HDL4 497
IV. Physiopathological Consequences of the Expansion 497
V. Conclusion 497
References 498
PART VIII Other Polyamino Acid Repeats 502
Chapter 33 Polyalanine and Polyglutamine Diseases: Possible Common Mechanisms? 504
I. Introduction 505
A. Noncoding Diseases 505
B. Coding Diseases 505
II. Polyglutamine Diseases 505
A. Common Features 505
B. Recent Molecular Mechanisms in PolyQ Disease Research: Lessons for PolyAla Disorders 506
C. Recent Treatment Advances in the PolyQ Disease Field 510
III. Polyalanine Disorders 510
A. Description 510
B. PolyAla Disorders: Examples and Recent Molecular Mechanisms 510
IV. Comparison of PolyAla and PolyQ Diseases: Similarities and Differences 515
A. Protein Aggregates 515
B. Beta-Sheet Structure of Expanded PolyQ and PolyAla Tracts 515
C. Gene Structure\u2013Function 516
D. Clinical Symptoms 516
E. Expansion Length 516
F. Mutational Mechanism 516
G. Age of Onset 516
H. Protein Intracellular Sublocalization 517
I. Loss versus Gain of Function 517
J. Cell Specificity 517
K. Ala Tract versus Q Tract 517
V. Oculopharyngeal Muscular Dystrophy and PolyQ Diseases 517
A. OPMD Background 517
B. PolyA Binding Protein Nuclear 1: OPMD Gene Product 518
C. Protein Aggregates in OPMD and PolyQ Diseases 518
D. OPMD Recent Molecular Mechanisms 518
E. Similar Molecular Mechanisms between OPMD and PolyQ Diseases 518
F. Treatment in OPMD and PolyQ Diseases 522
G. Intriguing Questions 522
VI. Conclusion 523
References 523
PART IX Biophysics of PolyQ 532
Chapter 34 Chemical and Physical Properties of Polyglutamine Repeat Sequences 534
I. Introduction 534
II. Chemical and Physical Properties of the Amino Acid Glutamine 535
III. Solubility and Conformations of the Polyglutamine Sequence 536
A. Conformations of Normal Repeat Length Polyglutamine 536
B. Conformation of Expanded Polyglutamine 537
IV. Normal Roles of the Polyglutamine Sequence in Proteins 537
A. Polyglutamine as a Flexible Linker between Secondary Structural Elements and Domains 537
B. Polyglutamine as a Solubilizing Domain 539
C. Polyglutamine as an Interaction or Aggregation Domain 539
V. Aggregation of Polyglutamine Sequences 540
A. Varieties of Polyglutamine Aggregates 541
B. Amyloid-like Aggregates with a Polyglutamine Core 541
C. Polyglutamine Protein Aggregation Not Related to a Polyglutamine Amyloid Core 546
D. Cellular Factors Influencing Aggregation 547
VI. Conclusions 547
References 548
PART X In Vivo Instability Studies 552
Chapter 35 Somatic Mosaicism of Expanded CAG cdot CTG Repeats in Humans and Mice: Dynamics, Mechanisms, and Consequences 554
I. Introduction 555
A. The CAG cdot CTG Repeat Expansion Loci 555
B. Why Are There So Many CAG CTG Repeat Disorders? 555
II. Dynamics of Somatic Mosaicism in Humans 556
A. Genotyping and Measurement of Somatic Mo 556
B. Somatic Mosaicism in Myotonic Dystrophy Type 1 558
C. Somatic Mosaicism in Huntington Disease 558
D. Somatic Mosaicism in Other CAG CTG Repeat Disorders 559
E. General Features of Somatic Mosaicism in Humans 559
III. Dynamics of Somatic Mosaicism in Human and Mouse Cell Models 560
A. Dynamics of Somatic Mosaicism in Human Tissue Culture 560
B. Dynamics and Tissue Specificity of Somatic Mosaicism in Transgenic Mice 560
C. Dynamics of Somatic Mosaicism in Mouse Tissue Culture 562
IV. Consequences of Somatic Mosaicism 562
A. Age-Dependent Allele Length Measurements 562
B. Does Expansion-Biased Somatic Mosaicism Contribute to Disease Pathology? 563
V. Cis-Acting Modifiers of Somatic Mosaicism 564
VI. Trans-Acting Genetic Modifiers of Somatic Mosaicism 565
A. DNA Mismatch Repair Genes Are Required To Generate Somatic Mosaicism 565
B. Other DNA Repair Pathways 566
C. Strain Effects 566
VII. What Is the Mechanism of Somatic Expansion? 566
A. Replication Slippage Is Not the Major Mechanism of Expansion 566
B. Are DNA Hairpins and/or Other Unusual Structures Mutation Intermediates? 568
C. Somatic Expansion Could Occur by Inappropriate DNA Mismatch Repair 568
VIII. Somatic Mosaicism as a Therapeutic Target 569
A. Can Repeat Expansion Be Modified by Drugs? 569
B. Is DNA Mismatch Repair a Therapeutic Target? 570
C. Somatic Mosaicism and Off-Target Drug Effects 570
IX. Concluding Remarks 571
References 571
Chapter 36 Transgenic Mouse Models of Unstable Trinucleotide Repeats: Toward an Understanding of Disease-Associated Repeat Size Mutation 580
I. Trinucleotide Repeats and Human Disease 581
II. Repeat Dynamics 581
A. Intergenerational Instability 581
B. Somatic Instability 582
III. Mouse Models of Repeat Instability 582
A. Initial Attempts 583
B. Cis Modifiers of Trinucleotide Repeat Instability 584
C. Trans-Acting Modifiers of Trinucleotide Repeat Instability 588
D. Timing of Repeat Instability 592
IV. Concluding Remarks 594
A. Recreation of Intergenerational Instability in Transgenic Mice 594
B. Recreation of Somatic Mosaicism in Transgenic Mice 595
References 596
PART XI Insect Models 602
Chapter 37 Drosophila Models of Polyglutamine Disorders 604
I. Introduction 604
II. Study of Neurodegeneration Using Genetic Approaches 605
III. Fly Models of Polyglutamine Diseases 605
A. Spinocerebellar Ataxia Type 3 (Machado\u2013Joseph Disease) 605
B. Huntington\u2019s Disease 607
C. Pure Polyglutamine Models 604
D. Spinocerebellar Ataxia Type 1 604
E. Spinobulbar Muscular Atrophy 604
IV. Modifiers of Fly Polyglutamine Models 604
References 604
PART XII Instability Mechanisms in Vivo and in Vitro 612
Chapter 38 Involvement of Genetic Recombination in Microsatellite Instability 614
I. Introduction 614
II. Trinucleotide Repeat Instability Associated with Recombination in Clinical Cases 615
III. Large CTG cdot CAG Expansions in Escherichia coli Are Caused by Gene Conversion 616
IV. Microsatellite Sequences Influence the Frequency of Recombination 617
A. Role of Non-B-DNA Structures Formed by Microsatellite Sequences in Recombination 617
B. CTG cdot CAG Repeats Expanded in Myotonic Dystrophy Type 1 Are Preferred Sites of Intramolecular and Intermolecular Recombination 618
C. Recombination Properties of the CCTG cdot CAGG Tetranucleotide Repeats Associated with Myotonic Dystrophy Type 2 621
D. Structure-Dependent Recombination Hot Spot Activity of GAA cdot TTC Sequences 623
V. Involvement of DNA Incisions (Breaks, Nicks, and Gaps) in Stimulation of Trinucleotide Repeat Sequence Instabilities 624
A. Role of Double-Strand Breaks in Genetic Instability 624
B. Effect of Single-Strand Nicks and Gaps on the Instability of CTG cdot CAG Repeats 625
VI. Concluding Remarks 627
References 628
Chapter 39 Bending the Rules: Unusual Nucleic Acid Structures and Disease Pathology in the Repeat Expansion Diseases 634
I. Introduction 634
II. Unusual Structures Formed by the DNA and RNA versions of the Disease-Associated Repeats 637
A. DNA Structures 637
B. RNA Structures 639
C. Effects of Interruptions 639
D. Evidence for Secondary Structures in Vivo 639
III. Potential Biological Consequences of These Unusual Structures 640
A. Expansion 640
B. Chromosome Fragility 642
C. Effects on Gene Expression 643
IV. Concluding Remarks 646
References 646
Chapter 40 Replication of Expandable DNA Repeats 654
I. Introduction 654
II. Experimental Approach 656
III. Main Experimental Results 657
IV. Replication Model for Repeat Expansions 658
V. Concluding Remarks 659
References 660
Chapter 41 Error-Prone Repair of Slipped (CTG)cdot(CAG) Repeats and Disease-Associated Expansions 662
I. Introduction 663
II. Slipped DNAs as Mutagenic Intermediates 663
A. Structure of Slipped DNAs 663
B. Repair of Heteroduplexes with Components of Slipped DNAs 666
III. Processing of Unpaired DNAs 667
A. Nucleotide Excision Repair and Repeat Instability? 667
B. Random-Sequence Heteroduplex Repair 667
C. Mismatch Repair and (CTG) cdot (CAG) Instability 667
IV. Binding of MMR Proteins to Trinucleotide Repeats 670
V. Processing of Slipped (CTG) cdot (CAG) Repeats by Human Cell Extracts 671
A. Three Repair Outcomes: Correct, Escaped, and Error-Prone Repair 672
B. Slipped-DNA Repair Is Independent of MMR and NER Proteins 673
C. Neuronlike Cell Extracts Process Slipped DNAs 674
D. Mechanism of Correct Repair 674
E. Mechanism of Escaped Repair 674
F. Mechanism of Error-Prone Repair 674
G. Comparison of Slipped (CTG) cdot (CAG) Processing with Base\u2013Base Mismatches and Random-Sequence Heteroduplexes 676
H. Role of Repair Proteins in (CTG) cdot (CAG) Instability? 677
I. Slipped-DNA Processing and Repeat Instability in Human Disease 678
V. Summary and Future Studies 679
References 679
Chapter 42 DNA Repair Models for Understanding Triplet Repeat Instability 684
I. Introduction and Background 684
II. Results and Discussion 688
III. Concluding Remarks 693
References 693
Chapter 43 Models of Repair Underlying Trinucleotide DNA Expansion 696
I. Introduction 696
II. General Considerations: Mechanisms of Expansion Based on Human Disease Data 696
III. Repair Rather Than Mitotic Replication 697
IV. Break Repair Mechanisms 700
A. Rescue of a Stalled Replication Fork by Recombination or Polymerase Reversal 700
B. Excision Repair 701
V. Emerging and Unresolved Issues:The Role of Mismatch Repair Proteins 703
References 704
Chapter 44 Transcription and Triplet Repeat Instability 708
I. Introduction 708
II. Tissue-Specific Variation in Repeat Tract Lengths in Humans and Mice 710
A. Genes Associated with Triplet Repeat Expansions Are Widely Expressed 710
B. Tissue-Specific Variation in Repeat Tract Length Is Common 710
C. Age-Dependent Repeat Instability Is Common, Even in Terminally Differentiated Neurons 712
III. Transcription and Repeat Instability in Bacteria,Yeast, and Human Cells 713
A. Transcription Destabilizes Triplet Repeat Sequences in Bacteria 713
B. Transcription Destabilizes Simple Sequence Repeats in Yeast 714
C. Transcription Destabilizes Triplet Repeats in Human Cells 715
IV. Concluding Remarks 716
References 717
Chapter 45 Structural Characteristics of Trinucleotide Repeats in Transcripts 722
I. Introduction 722
II. Simple Sequence Repeats in Genes and Proteins 723
III. Triplet Repeats in Transcripts 723
IV. Triplet Repeats in the Human Transcriptome 724
V. RNA Structures of Triplet Repeats 724
VI. RNA Structures of Triplet Repeats and Their Flanking Sequences 725
VII. Structural Role of the Repeat Interruptions 726
VIII. Cell Defense Systems Against dsRNA 728
IX. Concluding Remarks 728
References 729
PART XIII Mutations in Flanking Sequences 732
Chapter 46 Gross Rearrangements Caused by Long Triplet and Other Repeat Sequences 734
I. Introduction 734
II. Non-B-DNA Conformations Adopted by Triplet and Other Repeat Sequences 735
A. Slipped and Hairpin Structures 735
B. Cruciform DNA 737
C. Triplex DNA 737
D. Tetraplex DNA and i-Motifs 737
E. Left-Handed Z-DNA 738
III. Non-B-DNA and Gross Rearrangements in Model Systems 738
A. The 2.5-kb Poly(R cdot Y) Sequence of the Human PKD1 Gene 738
B. Myotonic Dystrophy Type 1 Triplet Repeat Sequence 739
C. Other Non-B-DNA-Forming Sequences 743
IV. DNA Structure and Human Disease 743
A. Statistical Analyses of Breakpoint Junction Sequences 743
B. Triplex DNA in Follicular Lymphomas 744
C. Segmental Duplications and Genomic Disorders 744
D. DNA Repair and Chromosomal Rearrangements 746
V. Summary and Concluding Remarks 747
References 747
PART XIV Cancer and Genetic Instability 752
Chapter 47 Microsatellite Instability in Cancer 754
I. Introduction 754
II. Microsatellite Instability (MSI) in Hereditary Nonpolyposis Color Cancer (HNPCC) 755
III. Downstream Impact of MSI on Cancer 756
IV. MSI-High HNPCC 756
V. HNPCC Tumors That Are Not MSI-High 757
VI. Alternate Bases for HNPCC in Non-MSI-High Tumors 757
A. Impact of Different DNA Repair Genes on MSI 757
B. Polymorphisms of Unknown Significance and HNPCC 758
VII. Increased Sensitivity of MSI Detection 758
A. Sensitive Technology Detects MSI in PBLs of MMR Mutation Carriers 758
B. Analysis of CRC Material by SP-PCR 759
C. Mutation in Constitutive Tissue of Carriers of DNA Repair Mutations 759
D. MSI Increases with Age in Normal Individuals 762
VIII. Conclusion 763
References 763
Index 766