RNA Processing: Disease and Genome-wide Probing (Advances in Experimental Medicine and Biology)

Description

Ribonucleic acid (RNA) binding proteins currently number in the thousands and defects in their function are at the heart of diseases such as cancer and neurodegeneration.  RNA binding proteins have become implicated in the intricate control of surprisingly diverse biological settings, such as circadian rhythm, stem cell self-renewal, oncogenesis and germ cell development. This book surveys a range of genome-wide and systems approaches to studying RNA binding proteins, the importance of RNA binding proteins in development, cancer and circadian rhythm.     Preface Contents Contributors Chapter 1: Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions 1 Background 2 What Is an RNA-Binding Protein? 3 Identification of RNA-Binding Protein Binding Sites In Vivo 4 Challenges of Peak Finding for RNA-Binding Proteins Compared to DNA Binding Proteins 5 RBP-Responsive RNA Targets 6 Choosing Between Depletion Versus Over-Expression Experiments 7 Quantitation of RNA Isoform Abundance 8 Identification of Altered RNA Splicing Events by Microarray 9 Quantifying Alternative Splicing by High-Throughput Sequencing 10 Identification of Novel Alternative Splicing Events by RNA-Seq and Microarray 11 Alternative Polyadenylation Sites 12 Transcriptome-wide Measurement of RNA Stability 13 Global Quantification of Ribosome Occupancy 14 Challenges of Scale 15 Learning Predictive RNA Processing Networks 16 Integrating Target Information to Generate Regulatory Maps for Individual RBPs 17 Integration of Multiple RBP Datasets 18 Conclusion References Chapter 2: Genome-Wide Approaches for RNA Structure Probing 1 Introduction 2 Classical RNA Structure Probing Methodologies 2.1 Nuclease-Based Approaches 2.2 Base Modification-Based Approaches 2.3 Backbone Modification-Based Methods 3 Nuclease-Based High-Throughput Approaches 3.1 Parallel Analysis of RNA Structures (PARS) 3.1.1 PARS Analysis in Saccharomy ces cerevisiae 3.1.2 PARS with Temperature Elevation 3.1.3 PARS Analysis of the Human Transcriptome, In Vitro and Native Dep roteinized 3.2 FragSeq 3.2.1 FragSeq on€Mouse Nuclear RNA 3.3 ds/ssRNA-Seq 3.3.1 dsRNA-Seq in€Arabidopsis thaliana RDR6 Mutants 3.3.2 ds/ssRNA-Seq in€Drosophila melanogaster and€Caenorhabditis elegans 3.3.3 ds/ssRNA-Seq in€Arabidopsis 3.3.4 Native Deproteinized ds/ssRNA-Seq in€Arabidopsis 4 Chemical-Based High-Throughput Approaches 4.1 Base Modification-Based High-Throughput Approaches 4.1.1 DMS-Seq in€Yeast and€Human Cells 4.1.2 Structure-Seq in€Arabidopsis 4.1.3 Mod-Seq in€Yeast 4.1.4 CIRS-Seq in€Mouse Embryonic Cells 4.2 SHAPE-Based High-Throughput Approaches 5 Conclusions and€Outlook References Chapter 3: Tethered Function Assays as Tools to Elucidate the€Molecular Roles of RNA-Binding Proteins 1 Introduction 2 Designing and€Performing Tethered Function Assays and€Interpreting Their Results 2.1 Constructs 2.2 Position and€Number of€the€Tethering Sites 2.3 Limitations, Controls, and€Interpretation 2.4 Follow-Up and Validation 3 Tethering Systems 3.1 MS2 3.2 λN 3.3 PP7 3.4 Iron Responsive Protein (IRP) 3.5 Qβ, GA, Tat/TAR, and U1A 4 Applications of€Tethered Function Assays 4.1 mRNA Stability 4.2 Translation 4.3 Pre-mRNA Splicing 4.4 RNA Transport and€Localization 5 Conclusions and€Outlook References Chapter 4: Single Molecule Approaches in RNA-Protein Interactions 1 Introduction 2 Single Molecule Investigation of€RNA-Protein Interactions 2.1 Why Look at Single Molecules? 2.2 Using Fluorescence Microscopy for€Single Molecule Imaging 3 Single Molecule Co-localization Spectroscopy (CoSMoS) 3.1 CoSMoS Instrumentation 3.2 CoSMoS: Practical Considerations 3.3 Fluorescent Proteins 3.4 SNAP and CLIP Tags 3.5 HaloTag 3.6 DHFR Tag 4 CoSMoS Data Analysis 5 Conclusions References Chapter 5: RNA Dynamics in the Control of Circadian Rhythm 1 Introduction 2 Circadian Regulation of Transcription Initiation 3 Circadian Regulation of Transcription Termination 4 Evidence for the Relevance of Posttranscriptional Events on Circadian Gene Expression 5 Circadian Regulation of Alternative Splicing 6 Circadian Polyadenylation 7 Regulation at Translation Initiation and Ribosome Biogenesis 8 RNA-binding Proteins Regulating mRNA Stability and Translational Efficiency Are Important for Oscillation of Core Clock Components 9 Conclusion References Chapter 6: Roles of RNA-binding Proteins and Post- transcriptional Regulation in Driving Male Germ Cell Development in the Mouse 1 Introduction 2 Male Germ Cell Development 2.1 Overview of Pathway 2.2 Embryonic Stages of Germ Cell Development 2.3 Postnatal Germ Cell Development 2.3.1 Spermatogonia Proliferation, Renewal, and Differentiation 2.3.2 Meiosis 2.3.3 Spermiogenesis (Spermatid Differentiation) 3 Complexity and Post-transcriptional Regulation of the Developing Germ Cell Transcriptome 3.1 Modulating Gene Output Via Alternative Splicing and Polyadenylation 3.2 Functional Consequences of Alternative Processing of Germ Cell mRNAs 3.2.1 LIG3, SOX17, and CREM 3.2.2 Different Fates for Alternatively Polyadenylated Germ Cell mRNAs 3.3 Translational Control: Global and Message-Specific 3.4 Post-transcriptional Control Through PolyA Tail Length Regulation 4 Roles of RNA-binding Proteins in Germ Cell mRNA Regulation 4.1 Elavl1/HuR 4.2 CELF (CUGBP, ELAV-Like Family) Proteins 4.3 Sam68 4.4 PTB (Polypyrimidine Tract Binding) Family of RBPs 4.5 τ-Cstf64 4.6 Y-Box Proteins 4.7 CPEB (Cytoplasmic Polyadenylation Element Binding Protein) 4.8 Pumilio and Nanos 4.9 Dazl 5 Conclusion References Chapter 7: Regulation of Stem Cell Self-Renewal and Oncogenesis by RNA-Binding Proteins 1 Stem Cell Systems in Tissue Homeostasis and Oncogenesis 1.1 Hematopoietic Stem Cells 1.2 Intestinal Stem Cells 1.3 Cancer Stem Cells 2 Developmental Signals Regulating Stem Cell Self-Renewal 3 RNA-binding Proteins: The Emerging Players in Stem Cell Regulatory Network 3.1 Heterogeneous Ribonucleoprotein E2 (hnRNP E2) 3.2 IGF2BP/IMP Family 3.3 Lin28 3.4 Musashi Family 3.5 HuR/Elav Family 3.6 FET Family 3.7 Eukaryotic Translation Initiation Factor eIF4E 3.8 PUF Family 4 Conclusion References Chapter 8: Controlling the Editor: The Many Roles of RNA-Binding Proteins in Regulating A-to-I RNA Editing 1 Introduction to RNA Editing 1.1 Influence of ADAR Protein Domains on A-to-I Editing 2 Identification of RNA Editing Sites 2.1 Transcriptome-Wide Identification of RNA Editing Sites 3 Regulation of ADAR Editing Activity 4 RNA-binding Proteins that Regulate RNA Editing 4.1 RNA-binding Proteins that Alter Editing and Splicing 4.2 Double-Stranded RNA-binding Proteins that Influence RNA Editing 4.3 Disease-Associated RNA-binding Proteins that Regulate RNA Editing 5 Conclusions References Chapter 9: Splicing Factor Mutations in Cancer 1 Introduction 2 Discovery of Splicing Factor Mutations in Hematologic Malignancies 2.1 SF3B1 2.2 U2AF1 2.3 SRSF2 2.4 ZRSR2 3 Additional Splicing Factors 4 Splicing Inhibitors 5 Summary References Chapter 10: Regulation of Tissue-Specific Alternative Splicing: C. elegans as a Model System 1 Introduction 1.1 Importance of Alternative Splicing in Generating Diversity, Specialization and Regulation 2 Mechanisms of Splicing 3 Regulation of Splice-Site Recognition: Auxiliary cis- Elements and Regulatory Factors 4 Splicing Factors and Tissue Specific Alternative Splicing 5 Importance of Alternative Splicing in Defining and Functionalizing Tissues 6 Constitutive and Alternative Splicing in C. elegans 7 Monitoring Alternative Splicing in C. elegans 8 Tissue Specific Alternative Splicing in C. elegans 8.1 Observing Tissue-Specific Alternative Splicing 8.2 Assigning Function to Tissue-Specific Isoforms 9 Cell-Specific Alternative Splicing Within Tissues 9.1 Observing Cell-Type Specific Alternative Splicing 10 RNA-binding Proteins and cis-Elements Controlling Cell Specific Alternative Splicing in C. elegans 11 Evolution of Tissue-specific Alternative Splicing in C. elegans 11.1 Evolutionary Characteristics of Alternative Splicing from Worm to Human 11.2 Evolution of Tissue-Specific Alternative Splicing 11.3 Conservation of Tissue-Specific Splicing Factors 12 Perspectives and Future Goals 12.1 Dynamic Regulation of Alternative Splicing in Response to Environmental Stimuli 12.2 Splicing Regulation at the Level of Single Cells During Animal Development References Chapter 11: RNA Granules and Diseases: A Case Study of Stress Granules in ALS and FTLD 1 A Cellular World of RNA Granules 2 Stress Granules 2.1 Molecular Composition 2.2 Proposed Functions 3 RNA Granule Formation via Multivalency and Intrinsically Disordered Regions 3.1 Multivalency 3.2 Intrinsically Disordered Regions 3.3 SG Assembly 3.3.1 Regulation by Chaperones 3.3.2 Regulation by Post Translational Modifications 4 ALS and FTLD: When Aggregation Goes Awry 4.1 SGs and Cytoplasmic Pathological Inclusions 4.2 FUS, TDP-43 and Neurodegenerative Pathogenesis 4.2.1 Mislocalization of FUS from the Nucleus to the Cytoplasm 4.2.2 Prionogenicity of FUS and TDP-43 4.2.3 Aggregation-Prone Mutations in FUS and TDP-43 4.2.4 Mislocalization Without Aggregation 4.3 Aggregation, Toxicity, and a Role for SGs 4.3.1 Neuron-Specific Toxicity 4.3.2 Stress and Inclusion Solubility 4.3.3 Disruptions to Endogenous TDP-43/FUS Function 4.4 TDP-43, FUS, and Oxidative Stress 5 Concluding Remarks Notes References Chapter 12: Post-Translational Modifications and RNA- Binding Proteins 1 Introduction 2 PTM-Mediated Regulation of Pre-mRNA Processing 2.1 Transcription 2.2 Splicing 2.3 Alternative Splicing 2.4 mRNA 5′ G-Capping and Decapping 2.5 RNA Editing 3 PTM Regulation of Subcellular Localization 3.1 Nuclear/Cytoplasmic Shuttling 3.2 RNA Granules, P-Bodies and Nuclear Speckles 3.3 Exosome 4 PTM Regulation of Translation 5 PTM Regulation of RNA Stability and Destruction 5.1 miRNA Related Repression 5.2 RNA Decay 6 Conclusion References Index