Erdmann / Barciszewski RNA Technologies and Their Applications

1. Auflage 2010
ISBN: 978-3-642-12168-5
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 452 Seiten

Reihe: RNA Technologies

RNA technologies are the driving forces of modern medicine and biotechnology. They combine the fields of biochemistry, chemistry, molecular biology, cell biology, physics, nanotechnology and bioinformatics. The combination of these topics is set to revolutionize the medicine of tomorrow. After more than 15 years of extensive research in the field of RNA technologies, the first therapeutics are ready to reach the first patients. Thus we are witnessing the birth of a very exciting time in the development of molecular medicine, which will be based on the methods of RNA technologies. This volume is the first of a series. It covers various aspects of RNA interference and microRNAs, although antisense RNA applications, hammerhead ribozyme structure and function as well as non-coding RNAs are also discussed. The authors are internationally highly respected experts in the field of RNA technologies.

Autoren/Hrsg.

Barciszewski, Jan

Erdmann, Volker A.

Inhaltsverzeichnis

1;RNA Technologies and Their Applications;3
1.1;Preface;5
1.2;Contents;9
1.3;Contributors;11
1.4;The Key Features of RNA Silencing;17
1.4.1;1 Introduction;18
1.4.2;2 RNA Silencing Effector as a Two-Component System;21
1.4.3;3 Small RNA Biogenesis;22
1.4.3.1;3.1 miRNAs and siRNAs;22
1.4.3.2;3.2 Dicer-Independent Pathways;24
1.4.3.2.1;3.2.1 piRNAs;24
1.4.3.2.2;3.2.2 Secondary siRNAs in Worm;26
1.4.3.3;3.3 Endo-siRNAs;27
1.4.4;4 RISC Loading, Sorting, and Target-Sensing of Small RNAs;28
1.4.4.1;4.1 Sorting by Precursor Structures;30
1.4.4.2;4.2 Sorting by the 5 Ends;31
1.4.4.3;4.3 Sorting by Dicer Processing Polarity;31
1.4.4.4;4.4 Target-Sensing;32
1.4.5;5 Safeguards for RNA Silencing Pathways;33
1.4.6;6 Effector Modes of RNA Silencing Pathways;34
1.4.7;7 Regulations of RNA Silencing Pathways;35
1.4.7.1;7.1 Processing;35
1.4.7.2;7.2 Modification;37
1.4.7.3;7.3 RISC Activity;37
1.4.8;8 Perspective;38
1.4.9;References;39
1.5;Selected Strategies for the Delivery of siRNA In Vitro and In Vivo;45
1.5.1;1 Introduction;47
1.5.2;2 Mechanism of RNA Interference;48
1.5.3;3 Naked Delivery of siRNA In Vitro;48
1.5.3.1;3.1 Cellular Uptake of Naked Nucleic Acids;48
1.5.3.2;3.2 The Phosphorothioate-Stimulated Cellular Delivery of siRNA;50
1.5.3.3;3.3 The siRNA-Peptide Conjugate Approach;51
1.5.3.4;3.4 Intracellular Release of siRNA: A Major Hurdle;54
1.5.4;4 CPP-Mediated siRNA Delivery;55
1.5.4.1;4.1 Cell-Penetrating Peptides;55
1.5.4.2;4.2 Selected Examples of CPP-Mediated siRNA Delivery;57
1.5.5;5 Selected Examples of siRNA Delivery In Vivo;63
1.5.6;6 Conclusions and Future Prospects;66
1.5.7;References;67
1.6;RNAi Suppression and Its Application;75
1.6.1;1 RNA Interference;77
1.6.2;2 RNAi-Directed Viral Immunity;81
1.6.3;3 Identification and Function Characterization of Viral RNAi Suppressors;84
1.6.3.1;3.1 Agrobacterium-Mediated Transient Suppression Assay;85
1.6.3.2;3.2 Reversal of Transgene-Induced Gene Silencing;86
1.6.3.3;3.3 Grafting Assay;86
1.6.3.4;3.4 Replication Rescue of Mutant Viruses Defective in RNAi Suppression;86
1.6.4;4 Function Mechanism of Viral RNAi Suppressors;88
1.6.4.1;4.1 Viral Suppressors that Bind Viral dsRNA to Interfere with viRNA Biogenesis;89
1.6.4.2;4.2 Viral Suppressors that Target Virus-Derived siRNA for RNAi Suppression;91
1.6.4.3;4.3 Viral Suppressors that Target RNAi Effectors for Suppression;93
1.6.4.4;4.4 Viral Suppressors that Suppress Systemic RNAi;95
1.6.5;5 RNAi Suppressors of Nonviral Origin;96
1.6.5.1;5.1 Suppression of RNAi by Bacterial Pathogens;96
1.6.5.2;5.2 Cellular RNAi Suppressors;98
1.6.6;6 Biotechnological Application of RNAi Suppressors;99
1.6.6.1;6.1 Enhance Gene Expression for Rapid Function Analysis and Mass Production of Valuable Protein;99
1.6.6.2;6.2 Serve as Molecular Tools to Probe Various RNAi-Directed Functions;100
1.6.7;Appendix;101
1.6.8;References;103
1.7;Strategies to Prevent siRNA-Triggered Cellular Toxicity;109
1.7.1;1 Introduction;110
1.7.2;2 Cellular Sensors of siRNA-Triggered Innate Immune Response;112
1.7.2.1;2.1 TLR-Mediated Innate Immunity;113
1.7.2.2;2.2 Non-TLR-Mediated Innate Immunity;113
1.7.3;3 Cellular Sequels After siRNA-Triggered Innate Immune System Activation;114
1.7.4;4 Overcoming Synthetic siRNA-Triggered Innate Immune Response;115
1.7.5;5 Overcoming shRNA-Triggered Innate Immune Response;116
1.7.6;6 shRNA-Mediated Disruption of the Endogenous miRNA Machinery;118
1.7.7;7 Conclusions;119
1.7.8;References;119
1.8;RNAi in Malignant Brain Tumors: Relevance to Molecular and Translational Research;123
1.8.1;1 Introduction;124
1.8.1.1;1.1 Diagnostic Characteristics of Diffuse Astrocytic Tumor;124
1.8.1.2;1.2 Clinical Course;125
1.8.1.2.1;1.2.1 Symptoms;125
1.8.1.2.2;1.2.2 Prognosis;126
1.8.1.3;1.3 Obstacles in Treatment of Diffuse Astrocytic Tumors;126
1.8.2;2 RNAi for Glioma: from Bench to Clinic;127
1.8.2.1;2.1 Preclinical Studies;128
1.8.2.2;2.2 Target Genes for Silencing;129
1.8.2.3;2.3 Problems in Clinical Translation;130
1.8.2.3.1;2.3.1 Specificity;131
1.8.2.3.1.1;Off-Target Effect;131
1.8.2.3.1.2;Interferon Response;131
1.8.2.3.2;2.3.2 Instability;132
1.8.2.3.3;2.3.3 Delivery;132
1.8.2.3.3.1;Systemic Route;133
1.8.2.3.3.2;Local Route;134
1.8.3;3 miRNAs in Glioma;135
1.8.3.1;3.1 Molecular Pathology of Aberrant miRNAs in Glioblastoma;136
1.8.3.1.1;3.1.1 Upregulated miRNAs;136
1.8.3.1.1.1;miR-21;136
1.8.3.1.1.2;miR-26a;136
1.8.3.1.1.3;miR-125b;136
1.8.3.1.1.4;miR-221-222 Cluster;138
1.8.3.1.1.5;miR-296;138
1.8.3.1.2;3.1.2 Downregulated miRNAs;138
1.8.3.1.2.1;miR-7;138
1.8.3.1.2.2;miR-15;139
1.8.3.1.2.3;miR-124 and miR-137;139
1.8.3.1.2.4;miR-128;139
1.8.3.1.2.5;miR-146b;139
1.8.3.1.2.6;miR-181 Family;140
1.8.4;4 Conclusions and Perspective;140
1.8.5;References;140
1.9;Silencing Huntington´s Disease Gene with RNAi;146
1.9.1;1 Introduction;147
1.9.2;2 A New Approach to Understanding Normal Function of Wild-Type Huntingtin;148
1.9.3;3 Nonallele-Specific Silencing of Huntingtin;150
1.9.4;4 Allele-Specific Silencing of Mutant Huntingtin;159
1.9.5;5 Current Challenges and Future Perspectives;163
1.9.6;References;170
1.10;Application of Dicer-Substrate siRNA in Pain Research;176
1.10.1;1 RNAi in Pain Research;177
1.10.2;2 Potential Applications of RNA Interference for Pain Treatment;178
1.10.2.1;2.1 Ion Channels as Therapeutic Targets for Pain;178
1.10.2.2;2.2 G-Protein-Coupled Receptors as Pain Targets;181
1.10.3;3 Advantages of DsiRNA Over Conventional siRNA;182
1.10.3.1;3.1 Inherent Character of DsiRNA;183
1.10.3.1.1;3.1.1 Dodging Nucleases Attack;183
1.10.3.1.2;3.1.2 Keeping ``On-Target´´;184
1.10.3.1.3;3.1.3 Eluding the Unpredictable;185
1.10.3.1.4;3.1.4 Sharing Is Not Always Best;185
1.10.3.2;3.2 Molecular Mechanism of Action;186
1.10.3.2.1;3.2.1 Initiation of RNAi Pathways: Role of DICER;186
1.10.3.2.2;3.2.2 Formation of RISC Loading Complex and Its Activation;187
1.10.3.2.3;3.2.3 Target Recognition by RISC and Gene Silencing;188
1.10.4;4 DsiRNA for Efficient Silencing In Vitro;189
1.10.4.1;4.1 Methodology;189
1.10.4.1.1;4.1.1 Design Rules;189
1.10.4.1.2;4.1.2 Cell Lineage Selection;190
1.10.4.1.3;4.1.3 Extensive Formulation Screening;190
1.10.4.1.4;4.1.4 Control Your Assay;191
1.10.4.2;4.2 Validation of Knockdown Efficiency;191
1.10.4.3;4.3 Targets In Vitro;192
1.10.5;5 DsiRNA In Vivo: One Step Forward;195
1.10.5.1;5.1 Working Evidence of DsiRNA In Vivo;195
1.10.5.1.1;5.1.1 Peripheral Organs;195
1.10.5.1.2;5.1.2 Central Organs;196
1.10.5.2;5.2 Methodology;196
1.10.5.2.1;5.2.1 Formulation;196
1.10.5.2.2;5.2.2 Uptake Validation;197
1.10.5.2.3;5.2.3 Molecular Silencing Confirmation;197
1.10.5.2.4;5.2.4 Assessing Specificity;198
1.10.5.2.5;5.2.5 Pain Assessment;199
1.10.6;6 Conclusion and Perspectives;201
1.10.7;References;203
1.11;RNAi Treatment of HIV-1 Infection;206
1.11.1;1 The RNAi Pathway for Expression of Therapeutic siRNAs;207
1.11.2;2 RNAi Gene Therapy Against HIV-1;209
1.11.3;3 Finding the Optimal Viral Target Sites;211
1.11.4;4 Combinatorial RNAi;212
1.11.5;5 Targeting Cellular Cofactors of HIV-1 Replication;212
1.11.6;6 Alternative Inhibitory RNA Molecules;213
1.11.7;7 Preclinical Test Systems;214
1.11.8;8 Sequence-Specificity of RNAi Action;214
1.11.9;9 Safety Issues Raised in Clinical Trials;215
1.11.10;10 Clinical Trials;216
1.11.11;11 Conclusion;216
1.11.12;References;217
1.12;Application of RNA Interference to Treat Conditions Associated with Dysregulation of Transient Receptor Potential Vanilloid 1 ;224
1.12.1;1 TRPV1 Ion Channels;226
1.12.2;2 Neuropathic Pain;227
1.12.2.1;2.1 Current Treatment;227
1.12.2.2;2.2 TRPV1 and Neuropathic Pain;227
1.12.2.3;2.3 Diabetic Peripheral Neuropathy;228
1.12.3;3 Drug-Induced Hearing Loss;229
1.12.3.1;3.1 TRPV1 and Cisplatin Ototoxicity;229
1.12.3.2;3.2 Utility of RNAi in Treating Cisplatin Ototoxicity;230
1.12.4;4 Other Potential Uses of RNAi Targeting TRPV1;232
1.12.4.1;4.1 Inflammation;233
1.12.4.2;4.2 Arthritis;233
1.12.4.3;4.3 Cystitis and Bladder Hyperactivity;234
1.12.4.4;4.4 Cancer Pain;235
1.12.4.5;4.5 Obesity;236
1.12.5;5 Conclusions;237
1.12.6;References;238
1.13;Harnessing RNAi-Based Functional Genomics to Unravel the Molecular Complexity Underlying Skin Pigment Variation;242
1.13.1;1 Melanin: A Ubiquitous Pigment with a Multitude of Functions;243
1.13.2;2 Melanogenesis: Insights Uncovered by the Detailed Analysis of Genetic Disorders of Pigmentation;245
1.13.3;3 An RNAi-Based Functional Genomics Approach to Identify Novel Regulators of Melanogenesis in Human Cells;248
1.13.4;4 Integration of Multiple Systems-Level Approaches to Uncover Additional Regulators of Melanogenesis in Our Functional Genomic.;252
1.13.5;5 Identification of Novel Pathways that Regulate the Transcription of Melanogenic Enzymes;256
1.13.6;6 Identification of Novel Pathways that Regulate Melanosome Biogenesis;259
1.13.7;7 Identification of Regulators of Human Pigment Variation;262
1.13.8;8 Identification of Pharmacologic Agents that Impact Melanin Accumulation;263
1.13.9;9 Concluding Remarks;264
1.13.10;References;264
1.14;mRNA Structure and its Effects on Posttranscriptional Gene Silencing;269
1.14.1;1 Introduction;270
1.14.2;2 A Structured Target Site Reduces AON and siRNA Activity In Vitro;271
1.14.3;3 Analysis of Binding Affinity to mRNA and Rate Dependencies on Concentration for AON and siRNA Activity;272
1.14.4;4 AON and siRNA Guide Strand Have Equal Affinity for the Target mRNA;275
1.14.5;5 AON and siRNA Display Apparent First and Zero Order Kinetics;275
1.14.6;6 For Full In Vitro Activity, siRNA Require Greater Target Site Accessibility Than AON ;277
1.14.7;7 A Double-Stranded Target Site Greatly Reduces In Vitro PTGS Activity;279
1.14.8;8 An AON That is More Effective Than the siRNA Against an Identical Target In Vitro is Less Effective Against the Same Target .;279
1.14.9;9 Discussion;282
1.14.10;10 Conclusions;286
1.14.11;References;287
1.15;Antisense RNA-Mediated Regulation of the p53 Tumor Suppressor;290
1.15.1;1 Antisense RNAs as Regulators of Gene Expression;291
1.15.2;2 Regulation of p53 at the mRNA Level;292
1.15.3;3 Wrap53;293
1.15.4;4 Future Perspectives;296
1.15.5;References;296
1.16;Antisense Oligonucleotides: Insights from Preclinical Studies and Clinical Trials;298
1.16.1;1 Introduction;300
1.16.2;2 Antisense Oligonucleotides in Cancer Treatment;302
1.16.2.1;2.1 BCL2 (B-cell CLL/lymphoma 2);302
1.16.2.2;2.2 XIAP (X-Linked Inhibitor of Apoptosis);304
1.16.2.3;2.3 Survivin, BIRC5 (Baculoviral IAP Repeat-Containing 5);304
1.16.2.4;2.4 CLU (Clusterin);305
1.16.2.5;2.5 TGFB2 (Transforming Growth Factor, beta 2);306
1.16.3;3 Application of Antisense Oligonucleotides in Noncancerous Diseases;307
1.16.3.1;3.1 Asthma;307
1.16.3.2;3.2 Cardiovascular Disease;307
1.16.3.3;3.3 Duchenne Muscular Dystrophy - Exon-Skipping Therapy;308
1.16.3.4;3.4 Virus Infections;309
1.16.4;4 Specificity of Antisense-Mediated Gene Silencing;310
1.16.5;5 Conclusion;312
1.16.6;References;313
1.17;What can the New Hammerhead Ribozyme Structures Teach us About Design?;317
1.17.1;1 Introduction to the Hammerhead Ribozyme;318
1.17.1.1;1.1 The Genomic Ribozymes;319
1.17.1.2;1.2 What is a Hammerhead Ribozyme;319
1.17.1.3;1.3 Minimal and Full-Length Hammerhead Ribozymes;319
1.17.1.4;1.4 Expanding Biological Context;322
1.17.2;2 Hammerhead Ribozyme Structures;323
1.17.2.1;2.1 Three-Dimensional Structure of Minimal Hammerhead Ribozymes;324
1.17.2.2;2.2 Three-Dimensional Structures of Full-Length Hammerhead Ribozymes;325
1.17.2.2.1;2.2.1 Schistosomal Hammerhead Structure;325
1.17.2.2.2;2.2.2 Satellite Viral Hammerhead Ribozyme Structure;327
1.17.3;3 Structure and Mechanism;329
1.17.3.1;3.1 Acid-Base Catalysis;329
1.17.3.2;3.2 Metal Ions?;330
1.17.3.3;3.3 Substrate Binding and Specificity;331
1.17.4;4 Hammerhead Structure, Function, and Design;332
1.17.4.1;4.1 Minimal Hammerheads;332
1.17.4.2;4.2 Full-Length Hammerheads;332
1.17.5;References;334
1.18;microRNA Biogenesis and its Impact on RNA Interference;336
1.18.1;1 The microRNA Biogenesis Pathway;338
1.18.1.1;1.1 microRNA Gene Transcription;338
1.18.1.2;1.2 microRNA Editing: Small Changes Affect Many Steps;338
1.18.1.3;1.3 pri-miRNA Cleavage by the Microprocessor Complex;339
1.18.1.3.1;1.3.1 Regulation of the Microprocessor;340
1.18.1.3.2;1.3.2 Primary miRNA Generation in Plants;342
1.18.1.4;1.4 Nuclear Export of the microRNA Precursors by Exportin-5;343
1.18.1.5;1.5 The RISC Loading Complex;344
1.18.1.6;1.6 Terminal Loop Removal by Dicer;345
1.18.1.6.1;1.6.1 Control Mechanisms of the Dicer Cleavage;346
1.18.1.7;1.7 Ago2 Jumps the Queue: Generation of the ac-pre-miRNA;346
1.18.1.8;1.8 miRNA Duplex Unwinding;347
1.18.1.9;1.9 Strand Selection: Who Becomes the Guide?;348
1.18.1.10;1.10 Mediators of RNA Silencing: The Argonaute Proteins;348
1.18.1.10.1;1.10.1 Regulation of Ago Activity and Ago-Mediated Silencing Mechanisms;350
1.18.1.11;1.11 Half-Life and Degradation of microRNA;351
1.18.2;2 Implication for RNAi Technology;351
1.18.2.1;2.1 Potentials and Challenges of siRNAs as a Tool;353
1.18.2.2;2.2 siRNA Versus shRNA;354
1.18.2.3;2.3 shRNA-miR Library: Transferring microRNA Structures to Synthetic shRNAs;354
1.18.2.4;2.4 Enhancement of RNAi by microRNA Biogenesis Factors;355
1.18.2.5;2.5 microRNA Biogenesis in Health and Disease: Basis for RNAi Therapy;357
1.18.2.6;2.6 Concluding Remarks;358
1.18.3;References;358
1.19;MicroRNAs in Epithelial Antimicrobial Immunity;366
1.19.1;1 Introduction;367
1.19.2;2 Abundant Expression of miRNAs in Epithelial Cells;368
1.19.3;3 Regulation of miRNA Expression in Epithelial Cells;369
1.19.4;4 MicroRNAs in the Regulation of Epithelial Antimicrobial Defense;371
1.19.4.1;4.1 MicroRNAs and Maintenance of Epithelial Barrier Integrity;371
1.19.4.2;4.2 MicroRNAs and Regulation of Epithelial Intracellular Signaling Pathways;372
1.19.4.3;4.3 MicroRNAs and Expression of B7-Costimulatory Molecules in Epithelial Cells;374
1.19.4.4;4.4 MicroRNAs in the Exosomes Released from Epithelial Cells;374
1.19.4.5;4.5 MicroRNAs-Mediated Antivirus Response in Epithelial Cells;374
1.19.5;5 Conclusion and Perspectives;375
1.19.6;References;376
1.20;Emerging Roles of Long Noncoding RNAs in Gene Expression and Intracellular Organization;379
1.20.1;1 Introduction;380
1.20.2;2 Intracellular Behaviors of ncRNAs Distinct from Those of mRNAs;380
1.20.3;3 Unique Pathways for Long ncRNA Biogenesis;382
1.20.4;4 ncRNA Functions in the Regulation of Gene Expression;384
1.20.4.1;4.1 Regulation of Transcription Factor Activity by Long ncRNAs;384
1.20.4.2;4.2 ncRNA Transcription Affects Adjacent Gene Expression;386
1.20.4.3;4.3 ncRNA Recruits or Modulates Epigenetic Factors on the Chromosome;388
1.20.4.4;4.4 ncRNAs Regulate Gene Expression at Posttranscriptional Steps;390
1.20.5;5 Structural Roles of ncRNAs;391
1.20.6;6 ncRNAs in Biomedical Research;394
1.20.7;7 Future Directions for ncRNA Research;394
1.20.8;References;396
1.21;Noncoding RNAs as Therapeutic Targets;402
1.21.1;1 RNA-Dependent Regulation of Gene Expression;403
1.21.1.1;1.1 Gene Regulation Through Epigenetic Mechanisms;404
1.21.1.2;1.2 Controlling Transcription Machinery Activity;406
1.21.1.3;1.3 Posttranscriptional Regulatory Mechanisms;408
1.21.2;2 The Medical Perspective: Noncoding RNAs in Human Diseases;410
1.21.2.1;2.1 MicroRNAs;410
1.21.2.2;2.2 mRNA-Like ncRNAs;413
1.21.2.3;2.3 Other Transcripts;415
1.21.3;3 NcRNA-Based Therapeutic Strategies;416
1.21.4;References;418
1.22;Noncoding RNAs at H19/IGF2 Locus: Role in Imprinting, Gene Expression, and Associated Pathologies;428
1.22.1;1 The H19/IGF2 Locus and the Parental Imprinting Model;429
1.22.1.1;1.1 Overview and Description of the 11p15.5 Locus;429
1.22.1.2;1.2 The Insulator Model of Imprinting;433
1.22.1.2.1;1.2.1 DNA Methylation of H19 and IGF2 Genes;433
1.22.1.2.2;1.2.2 Histone Modifications at the H19/IGF2 Locus;434
1.22.1.2.3;1.2.3 The ICR or Imprinting Control Region;434
1.22.1.2.4;1.2.4 Imprinting and Parental Specific Chromatin Loops;436
1.22.2;2 The mRNA-Like Noncoding RNA H19;437
1.22.2.1;2.1 Properties and Expression;438
1.22.2.2;2.2 Functions;439
1.22.2.3;2.3 Regulation;439
1.22.3;3 The Noncoding Antisense RNA 91H;440
1.22.3.1;3.1 Characterization;440
1.22.3.2;3.2 Hypothesis About 91H Mechanism of Action;441
1.22.4;4 H19/IGF2 Locus-Associated Pathologies;442
1.22.4.1;4.1 Hormone-Dependent Cancers (Breast, Uterus);442
1.22.4.2;4.2 Children Syndromes;444
1.22.5;5 Conclusion;445
1.22.6;References;445
1.23;Index;453