RNA Biology: An Introduction

Preface

PART I: mRNA Biology

INTRODUCTION
RNA Building Blocks
RNA Folding
The RNA World Hypothesis
Functions of RNA
Protein Classes that are Required for RNA Function
TRANSCRIPTION OF PRE-mRNAs
Structure and Organization of Protein Coding Genes
Transcription of mRNAs by RNA Polymerase II
Transcriptional Termination of Pre-mRNAs
Transcription is Coupled to Other mRNA Maturation Steps
Summary
CAPPING OF THE PRE-mRNA 5' END
m7 G-cap Structure
mRNA Capping Enzymes
5' Capping is Coupled to Transcription
5' Cap Binding Proteins
Summary
3' END PROCESSING OF PRE-mRNAs
Polyadenylation Signals
Proteins Involved in 3' End Processing of Pre-mRNAs
3' End Processing is Tightly Linked to Transcriptional Termination
Alternative Polyadenylation
Cytoplasmic Polyadenylation
3' End Processing of Histone mRNAs
Summary
SPLICING OF EUKARYOTIC PRE-mRNAS
Group I, II and III Introns
The Mechanism of pre-mRNA Splicing
The Spliceosome
The U12-Dependent Minor Spliceosome
Coupling of Splicing with Transcription and 5' Capping
Alternative Splicing and the Complexity of Genomes
Summary
Questions
mRNA EXPORT FROM THE NUCLEOUS TO THE CYTOPLASM
Nuclear Import and Nuclear Export
mRNA Export Receptors
Adaptors the Bridge mRNAs with Export Receptors
Mechanism of mRNA Export
Coupling of mRNP Export to Other Steps of mRNA Maturation
Summary
Questions
TRANSLATION
Amino Acids, mRNAs, tRNAs
THe Ribosome
The Mechanisms of Translation
Translational Regulation
Coupling Translation with Other mRNA Maturation and Quality Control Steps
Summary
Questions
DEADENYLATION OF mRNA
Deadenylating Enzymes
Summary
Questions
mRNA DECAPPING
Decapping Enzymes are the Core of the mRNA Decapping Machinery
Scavenger Decapping Enzyme DcpS
Regulation of mRNA Decapping
Intracellular Localization of mRNA Decapping
Summary
Questions
mRNA DECAY PATHWAYS
Deadenylation-Dependent mRNA Decay
Deadenylation-Independent mRNA Decay
Endoribonuclease-Mediated mRNA Decay
Regulation of mRNA Decay
RNA Degradation in Bacteria
Summary
Questions
mRNA QUALITY CONTROL
Nuclear mRNA Quality Control Mechanisms
Nonsense-Mediated mRNA Decay (NMD)
Other nRNA Quality Control Pathways
Summary
Questions

PART II: Non-Coding RNA Biology

RIBOSOMAL RNAS AND THE BIOGENESIS OF RIBOSOMES
Genomic Organization of Ribosomal RNA Genes
Transcription of Ribosomal RNA Genes
Maturation of rRNAs
Nuclear Export of Ribosomal Subunits
Modification, Structure and Fucntion of rRNAs
Summary
Questions
TRANSFER RNAS
Genomic Organization and Transcription of tRNA Genes
Processing to Mature tRNAs
tRNA Modifications
Nuclear Export of tRNAs
Tertiary Structure of tRNAs
Summary
THE 7SL RNA AND THE SIGNAL RECOGNITION PARTICLE
Architecture of the SRP
SRP-Mediated Protein Translocation
Summary
REGULATION OF TRANSCRIPTION: THE 7SK SMALL NUCLEAR RNA
Architecture of the 7SK snRNA
The 7SK snRNP Functions as Transcriptional Regulator
Other Small Non-Coding RNAs that Interfere with Transcription
Summary
SMALL NUCLEOLAR RNAS
Genomic Organization and snoRNA Transcription
Box H/ACA snoRNAs
Box C/D snoRNAs
Maturation of Functional snoRNPs
Orphan snoRNAs
The Telomerase RNP
Summary
SPLICEOSOMAL SMALL NUCLEAR RNAS
Transcription and Maturation of Spliceosomal snRNAs
The Structure of UsnRNPs
Assembly of Spliceosomal snRNPs
Summary
Questions
SMALL NON-CODING RNAS AND THE MECHANISM OF GENE SILENCING
Short Interfering RNAs and the Mechanism of RNA Interference
Dicer
RNA-Dependent RNA Polymerases
Argonaute Proteins
microRNAs and the Regulation of Gene Expression
PiRNAs and the Regulation of Mobile Genetic Elements in the Germ Line
Small RNAs with Functions in Chromatin Regulation
The CRISPR System -
A Bacterial and Archaeal Defense Mechanism
Summary
LONG NON-CODING RNAS
The XIST Non-Coding RNA and X Chromosome Inactivation
Dosage Compensation n Flies
Non-Coding RNAs and the Regulation of Imprinting
The Regulation of HOX Genes by Long Non-Coding RNAs
Long Non-Coding RNAs are Common in Complex Genomes
Summary
RNA EDITING
RNA Editing by U Insertions or Deletions
RNA Editing by Base Modification
Summary
RIBOZYMES -
CATALYTIC RNA MOLECULES
Identification of Catalytic RNAs
Mechanisms and Secondary Structures of Different Ribozymes
Summary
RIBOSWITCHES AND RNA SENSORS
Mechanisms of Riboswitch Function
Riboswitch Structures
RNA Thermometers
Summary
RNOMICS
"Omics" Approaches
Experimental RNA Profiling Strategies
RNA Biology and the Complexity of Genomes
Summary
APPENDIX
Answers to Questions