RNA Structure and Function (RNA Technologies, 14)

✍ Scribed by Jan Barciszewski (editor)

• Publisher: Springer
• Year: 2023
• Tongue: English
• Leaves: 662
• Category: Library

✦ Synopsis

This book focuses on the current status of our understanding of RNA, a key biological molecule. The various RNAs covered are messenger RNA, ribosomal RNA, transfer RNA, noncoding RNAs, modified nucleosides, and RNA enzymes. The different chapters detail methods to investigate RNA structure and function, the chemistry of modified RNAs, and the latest advances in our understanding of the vast array of biological processes in which RNA is involved.

RNA, in one form or another, touches almost everything in a cell. RNA has both structural and catalytic properties. RNA fulfills a broad range of functions. These molecules are no longer seen as passive elements transferring the genetic information from DNA into proteins but regulate the activity of genes during development, cellular differentiation, and changing environments. RNAs are involved in various aspects of cell physiology and disease development. Discoveries of RNA with unexpected diverse functions in healthy and diseased cells,such as the role of RNA as both the source and countermeasure to cancer or severe viral infection, stimulate new trends, passion, and solutions for molecular medicine.

In this book, fundamental questions about the biochemical and genetic importance of RNA, how mRNAs are generated and used to produce proteins, how noncoding and catalytic RNAs mediate key cellular processes, how to determine RNA structure and how to apply RNA in treatment of diseases.

This book is an essential resource for researches in academia and industry contributing to the development of new RNA therapeutics. The book is geared toward scientists from the graduate level on up and particularly appeals to active investigators in RNA biology, molecular biology, and biochemistry.

✦ Table of Contents

Introduction
Contents
Transfer RNA Fragments, from Structure to Function
1 Introduction
2 tRF Biosynthesis
3 tRNA Halves (tiRNAs)
3.1 5′ tiRNAs Inhibit Translation
3.2 5′ tiRNAs Are Intercellular Communicating RNAs
3.3 5′ tiRNAs Modulate Epigenetic Inheritance
3.4 Both 5′ and 3′ tiRNAs Inhibit Apoptosis
4 Type I tRFs: miR-Like tRNA Fragments
4.1 Are MicroRNAs and tRFs Processed in the Same Way?
4.2 Gene Silencing by Short tRFs
4.3 Leucine Derived 3′ Short tRF Enhances Translation
5 Type II tRFs
6 Internal tRFs (i-tRFs)
7 Mitochondrial Genome-Originated tRFs
8 Involvement of tRFs in Brain Disorders
9 Methodology Used to Study tRFs
10 Conclusions
References
Detection of RNA Structure and Interactions Using Nanopore Technology
1 Introduction
2 Extracting Global Features of RNA Molecules from Nanopore Translocation Experiments
2.1 RNA Detection and Sensing
2.2 Investigation of RNA Folding
3 Deciphering RNA Interactions with Nanopore Sensing
3.1 RNA–Small Molecule Interaction
3.2 RNA–Protein Interaction
3.3 RNA–Ribosome Interaction
3.4 Engineering RNA-Interaction and Structure for Molecular Identification
4 RNA Structure Probing with Nanopore Sequencing
4.1 Chemical Probing and Direct RNA Sequencing for RNA Structural Probing
5 Conclusion
References
Mapping In Situ RNA–RNA Interactions with RIC-seq
1 Introduction
2 Methods for Probing RNA–RNA Interactions
2.1 Low-Throughput Methods
2.2 High-Throughput Methods
3 Global Profiling In Situ RNA–RNA Interactions with RIC-seq
3.1 Materials
3.2 Methods
3.3 Notes
4 Conclusion
5 Future Perspectives
References
Unraveling RNA by Mechanical Unzipping
1 Introduction
2 The Power of Single RNA Manipulation
2.1 SmFRET Experiments
2.2 Nanopore Microscopy
2.3 Optical Tweezers
3 RNA Pulling in a Nutshell
3.1 Brief History of RNA Pulling Experiments
4 RNA Energetics at 0.1 kcal/mol Accuracy
4.1 The RNA Free Energy of Formation
4.2 Salt Dependency of the Hybridization Free Energy
5 RNA Folding Kinetics
6 Future Perspectives
References
Structured RNAs and Their Role in Biology and Therapeutics
1 Introduction
2 Structure and Catalytic Function of Small Self-Cleaving Ribozymes
2.1 Hammerhead Ribozyme
2.2 Hairpin Ribozyme
2.3 Varkud Ribozyme
2.4 Twister Ribozyme
3 Riboswitches
3.1 Purine Riboswitch
3.2 GlmS Riboswitch/Ribozyme
3.3 Thiamine Pyrophosphate (TPP) Riboswitch
4 Targeting Riboswitches as an Antibacterial Strategy
4.1 Ribocil
4.2 Pyrithiamine
5 Conclusion
References
RNA Versus Protein, How Structure Influences Targeting, a New Challenge for Drug Discovery
1 Introduction to RNA Structures
2 RNA Higher Order Structures
3 Biophysical Techniques to Measure and Characterize RNA Secondary Structures
3.1 Physical Methods
3.2 Enzymatic-Based and Chemical-Based Methods
4 Biophysical Techniques to Measure and Characterize RNA Tertiary and Higher Order Structures
4.1 X-ray Crystallography and Small-Angle X-ray Scattering (SAXS)
4.2 Nuclear Magnetic Resonance (NMR)
4.3 Cryogenic Electron Microscopy (Cryo-EM)
5 Next Generation Sequencing Methods to Identify RNA Structures
6 Conclusions
References
Probing the RNA Structure-Dependent RNA Regulations and Functions
1 Introduction
2 RNA Structure-Probing Methods
3 Relationship Between RNA Structures and RNA Function
4 Cellular Internal Environment Elements That Affect RNA Structures
5 Challenges and Future Directions
References
Probing Techniques of Secondary and Tertiary RNA Structure and a Case Study for RNA G-Quadruplexes
1 Introduction
2 Secondary and Tertiary RNA Structure
2.1 Hierarchical Folding of RNA
2.2 Examples of Tertiary Structure Motifs
3 Techniques to Study RNA Secondary Structure
3.1 RNA Structure Prediction in Silico
3.2 Enzymatic Probing Techniques
3.3 Chemical Probing Techniques
4 Probing Techniques to Study the RNA G-Quadruplex Motif
4.1 In Silico Prediction of G4s
4.2 Visualisation of RNA G4s by Immunolabelling
4.3 Chemical Probing of RNA G4s Coupled to Sequencing
4.4 Immunoprecipitation of RNA G4s
4.5 Visualisation of RNA G4s with Fluorescent Probes
4.6 Disruption of G4 Structures with Antisense Oligonucleotides
5 Conclusion
References
Structure and Functions of RNA G-quadruplexes
1 Introduction
2 DNA G4s (dG4s) Versus RNA G4s (rG4s)
3 Functions of rG4s in the Nucleus
3.1 Transcriptional Regulation
3.2 mRNA Maturation
3.3 Non-coding RNA Maturation in the Nucleus
4 RNA Transport
5 Functions of rG4s in the Cytoplasm
5.1 Translation Regulation
5.2 mRNA Stability
5.3 ncRNA Biology
6 rG4 Binding Proteins
7 RG4s and Membrane-Less Biomolecular Condensates
8 rG4s as Therapeutic Targets
9 Concluding Remarks
References
Structure and Folding Patterns of RNA G-Quadruplexes
1 Introduction
2 Biological Roles of RNA Quadruplex
3 Topological Diversity of RNA Quadruplex
3.1 Helical Twist and Rise of the RNA Quadruplex Folds
3.2 Sugar-Phosphate Backbone and Glycosyl Conformational Angle Preferences
3.3 Fold-Dependent Water Network in RNA Quadruplex
3.4 Quartet‒Ion Interaction in RNA Quadruplex
4 Biophysical Techniques to Identify the Folding Nature of RNA Quadruplex
5 In Vitro and in Vivo Techniques to Identify RNA Quadruplex-Forming Regions
6 G–Quadruplex Prediction Tools
7 Modeling of RNA G-Quadruplex and Capturing Their Conformational Dynamics
8 Challenges in the Prediction and Modeling of RNA G-Quadruplexes
References
Methods to Analyze Post-transcriptional Modifications Applied to Stable RNAs in Staphylococcus aureus
1 Introduction
2 RNA Purification
2.1 Isolation of Total RNA from S. Aureus
2.2 Purification of rRNAs and tRNAs
2.3 Purification of Individual tRNAs
3 Mass Spectrometry to Identify and Localize Modifications in RNAs
3.1 Analysis of Nucleosides
3.2 Analysis of Oligonucleotides
4 Biochemical Analyses to Easily Map Specific RNA Modifications
4.1 Primer Extension
4.2 Nucleotide Derivatization Coupled to Primer Extension Analysis
4.3 Affinity Gels
5 RNA-seq to Map Modifications on Single RNA and Complexed RNA Samples
5.1 AlkAnilineSeq
5.2 HydraPsiSeq
5.3 RiboMethSeq
5.4 RNA BisulfiteSeq
5.5 Analysis of RT Signatures (RT-seq)
6 Analysis of rRNA Modifications Using Cryo-EM Structural Studies
7 Discussion
References
Bacterial Small RNAs: Diversity of Structure and Function
1 Introduction
2 sRNA that Use the 5′ Domain to Interact with mRNA Targets
3 sRNA that Use the 3′ Domain to Interact with mRNA Targets
4 sRNA Association with the RNA Chaperone Hfq
5 sRNAs that Bind to Proteins: The Example of CsrB
6 Sponge RNAs that Regulate sRNA Levels
6.1 Intergenic Region of the chbBC Transcript
6.2 3′ETSLeuZ
6.3 SroC
7 3′-UTR-Derived sRNAs
8 CRISPRs
9 Conclusions
References
A Moveable Feast. Molecular Modeling and Simulation Unraveling Cross-Talks Between RNA Structure and Its Biological Role
1 Introduction
1.1 RNA Structures and Biological Role
1.2 Stem Loops
1.3 Guanine Quadruplexes
2 Molecular Modeling and Simulations
3 Modeling RNA/Protein Interactions
3.1 Cellular Signal Pathways IRE/IRP
3.2 Organization of Viral Genome in SARS-CoV-2
3.3 Immune Response System and Selectivity of OAS
4 Perspectives Towards Therapeutic Strategies
References
Viroids: Non-coding Circular RNAs Are Tiny Pathogens Provoking a Broad Response in Host Plants
1 Introduction
2 Structure of Viroids
2.1 Structure of PLMVd
2.2 Structure of PSTVd
3 Replication of Viroids
3.1 Replication of Members of Avsunviroidae
3.2 Replication of Members of Pospiviroidae
4 Trafficking of Viroids
5 Plant Response to Viroid Infection
References
Biology of Circular RNAs and Methodological Approaches to Their Study
1 Introduction
2 Biogenesis and CircRNA Subtypes
3 Export and Turnover
4 Biological Functions
4.1 MiRNA Sponging
4.2 CircRNA–Protein Interaction
4.3 Translation of CircRNAs
5 Profiling and Analysis of CircRNAs
5.1 Purification and Enrichment of CircRNAs
5.2 Bioinformatic Approaches on CircRNAs and Their Global Profiling
5.3 PCR-Based Analyses
6 CircRNAs as Potential Biomarkers in Human Cancers
7 Perspective
References
Computational Tools for Functional Analysis of Circular RNAs
1 Introduction
2 Tools
3 Method
3.1 Finding the Mature CircRNA Sequence
3.2 Analysis of RBPs Interacting with circAkt3
3.3 Analysis of circRNA-miRNA-mRNA Regulatory Networks
3.4 Analysis of the Protein-Coding Potential of circAkt3
4 Technical Notes
References
The Hidden Layer of RNA Variants
1 Introduction
2 Noncoding RNAs
2.1 Nuclear LncRNAs
2.2 Enhancer RNAs
2.3 Gene Region Edge-Associated Transcripts
3 RNA Surveillance and RNA Quality Control
4 Nuclear RNA Decay Factors
4.1 XRN2
4.2 RNA Exosome
4.3 Nuclear Cofactors of RNA Exosome
4.4 TRF4-2-ZCCHC7-MTR4 Polyadenylation (TRAMP) Complex
4.5 Nuclear Exosome-Targeting (NEXT) Complex
4.6 Poly(A) Exosome-Targeting (PAXT) Connection
4.7 HNRNPH1
5 Concluding Remarks
References
Functional Role of Non-coding RNAs in Prostate Cancer: From Biomarker to Therapeutic Targets
1 Introduction
2 Structural Variations in Different NcRNAs
2.1 Structural Features of LncRNAs
2.2 Structural Features of MiRNAs
2.3 Structural Features of CircRNAs
3 Clinical Implications of Non-coding RNAs in Prostate Cancer
4 Non-coding RNA as Biomarker
4.1 LncRNAs
4.2 MiRNAs
4.3 CircRNAs
5 Non-coding RNA and Drug Resistance in Prostate Cancer
5.1 Non-coding RNAs and Anti-Androgen Resistance
5.2 Non-coding RNA’s Impact in Chemotherapy Resistance
6 Non-coding RNA as Therapeutic Target
7 Future Perspectives
8 Conclusions
References
The Structure, Function, and Modification of Non-coding RNAs in Cardiovascular System
1 Introduction
2 Overview of lncRNA, miRNA, circRNA, and RNA Modification
2.1 lncRNAs
2.2 miRNAs
2.3 circRNAs
2.4 RNA Modification
3 Functions of lncRNA, miRNA, circRNA, and RNA Modification in Pathological Processes of CVDs
3.1 Cardiac Hypertrophy (CH) and Heart Failure (HF)
3.2 Myocardial Infarction (MI) and Ischemia–Reperfusion Injury (I/RI)
3.3 Diabetic Cardiomyopathy (DCM)
3.4 Atherosclerosis (AS)
3.5 Other Cardiovascular Diseases
4 Conclusion and Perspective
References
Contribution of RNA Species in Sexually Transmitted Infections
1 Introduction
2 Mode of Action
3 Sexually Transmitted Infections
3.1 Viral
3.2 Bacterial
4 microRNA and lncRNA Interactions
5 ncRNA Therapeutic Interventions
6 Discussion
References
Hypoxia and Epithelial-to-Mesenchymal Transition (EMT) in Cancer: A Non-coding RNA Perspective
1 Introduction
2 Non-coding RNAs: Structure and Function
2.1 microRNAs
2.2 lncRNAs
2.3 Other Non-coding RNAs
3 EMT Signaling and Cancer
4 Hypoxia Signaling and Cancer
5 Hypoxia-Induced EMT and the Cancer Pathway Crosstalk
6 Non-coding RNAs Governing EMT and Hypoxia
6.1 miRNAs Governing Cancer EMT and Hypoxia
6.2 lncRNAs Governing Cancer EMT and Hypoxia
6.3 Other ncRNAs Governing Cancer EMT and Hypoxia
7 Non-coding RNAs as Therapeutics and Novel Biomarkers
8 Conclusions
References
A Study on the Role of piRNAs in Cancer Epigenetics
1 Introduction
2 Argonaute and PIWI Proteins
3 piRNA Biogenesis
3.1 Transcription of Uni-strand and Dual-Strand piRNA Cluster and Their Nuclear Processing
3.2 Maturation of Precursor piRNA
4 Functions of piRNAs
4.1 Silencing of Transposons
4.2 Gene Regulation and Development
4.3 Changes in Diseases
5 Epigenetic Mechanisms
6 piRNAs in Cancer
7 PIWI Expression in Cancer
8 Therapeutic Approach of piRNAs and PIWI Proteins
9 Conclusion
10 Competing Interests
References
Modified Nucleosides as RNA Components. Structure, Biological Role and Drug Design
1 Carbohydrate-Modified Nucleoside Derivatives
2 Base-Modified Nucleoside Derivatives
2.1 Purine-Modified Nucleosides
2.2 Pyrimidine-Modified Nucleoside Derivatives
2.3 Cellular Pathological States and Metabolic Disorders Associated with Minor Nucleosides
2.4 Isolation and Quantification of Minor RNA Components
3 Modified Nucleosides and Drug Design
4 Conclusions
References
Multifaceted Functions of RNA m6A Modification in Modulating Regulated Cell Death
1 Introduction
2 Apoptosis
2.1 M6A Regulates Intrinsic Signaling Pathways Dependent Apoptosis
2.2 M6A Regulates Extrinsic Signaling Pathway-Induced Apoptosis
2.3 Clinical Significance of m6A Regulating Apoptosis
3 Autophagy
3.1 M6A Modification Promotes Autophagy
3.2 M6A Modification Inhibits Autophagy
3.3 Autophagy Reversely Regulates m6A Related Molecules
4 Necroptosis
5 Pyroptosis
5.1 M6A Modification Promotes Pyroptosis
5.2 M6A Modification Inhibits Pyroptosis
5.3 Treatment of Pyroptosis-Mediated Adverse Effects by Regulating m6A Modification
6 Ferroptosis
6.1 M6A Modification Promotes Ferroptosis
6.2 M6A Modification Inhibits Ferroptosis
6.3 M6A Modification Regulates Ferroptosis in Various Diseases
7 Concluding Remarks
References
Incorporation of Pseudouridine into RNA for Biochemical and Biophysical Studies
1 Introduction
2 Pseudouridine
3 Synthesis of Pseudouridine
3.1 Organic Synthesis of Pseudouridine
3.2 Enzymatic Synthesis of Pseudouridine
3.3 Semi-Enzymatic Synthesis of Pseudouridine
4 Incorporation of a Modified Nucleotide into RNA Sequence
4.1 In Vitro Transcription
4.2 Solid-Phase Synthesis
5 Conclusions
References
Molecular Dynamics Simulations of Chemically Modified Ribonucleotides
1 Introduction
2 Molecular Dynamics Simulations
2.1 Standard Molecular Dynamics Simulations
2.2 Force Fields for Chemically Modified Nucleotides
2.3 Enhanced Sampling Methods
2.4 Alchemical Methods
3 Applications
3.1 Validation and Fitting of Force Fields Against Experimental Data
3.2 Effects of Post-transcriptional Modifications on RNA Structure and Dynamics
3.3 Effects of Post-transcriptional Modifications on Interaction with Proteins
3.4 Molecular Dynamics Simulations of Synthetic Nucleic Acids
4 Discussion and Challenges Ahead
References
Ribonucleases for Sequencing and Characterization of RNA by LC–MS
1 Introduction
2 Analytical Strategies for Sequencing and Modification Analysis of Synthetic RNA
3 Application of Endoribonucleases in RNA Analysis
4 Novel Endoribonuclease Strategies to Improve Sequence Mapping
5 Synthetic mRNA 5′ Cap Analysis
5.1 Deoxyribozymes
5.2 Trans-Cleaving Ribozymes
5.3 RNase H
6 Poly(A) Tail Analysis in Synthetic mRNA
7 Conclusions and Outlook
References
RNA-Processing DNAzymes
1 Introduction
1.1 Background and Applications
1.2 DNAzyme Diversity
2 Molecular Structure and Requirements Underlying RNA-Processing
2.1 The Catalytic Core Module
2.2 The RNA-Recognition Module
3 Activity in Cells
4 Conclusions and Outlook
References
RNA Nanotechnology for Chemotherapy and Immunotherapy
1 Introduction to RNA Nanotechnology
2 RNA Conjugation to Make Hydrophobic Drugs More Soluble
3 The Dynamic and Motile Nature of RNA Make Them Efficient in Specific Cancer Targeting
4 The Dynamics and Motile Nature of RNA Make Them Quick in Renal Excretion
5 Methods for Conjugating Chemical Drugs to RNA
6 Bispecific RNA Nanoparticles for Cancer Treatment
7 RNA Aptamers as Antibody to Regulate Immune Check Point in Cells Such as Treg Cells
8 New Technology to Display T Cell Ligands on Cancer Cells
9 Summary and Perspectives
References