Small RNAs

by Nellen, Wolfgang; Hammann, Christian

• ISBN13: 9783540742708
• ISBN10: 3540742700
• Edition: 1st
• Format: Paperback
• Copyright: 2007-12-04
• Publisher: Springer Verlag

Summary

In recent years Molecular Biology has experienced an unprecedented revolution by the discovery of functional small RNAs. The number of cellular processes in which non-coding RNAs are involved is growing rapidly and include gene regulation on the transcriptional, post-transcriptional and translational level. To complicate matters, these processes seem to be strongly interconnected on the one hand, and diverse among different organisms on the other. This volume describes strategies for the discovery and validation of small RNAs and provides a snapshot of our current understanding of the different mechanisms triggered by small RNAs.

Table of Contents

Small Regulatory RNAs in Bacteria	p. 1
Introduction	p. 1
Searches and Discovery of sRNAs	p. 2
The Early Years	p. 3
Modern-Day sRNA Gene Searches	p. 4
The Old and New Ones-Biological Functions	p. 5
Many sRNAs Are Involved in Stress Response Regulation	p. 7
What's Out There in Other Bacteria?	p. 13
Regulation of Virulence	p. 13
sRNAs and Quorum Sensing	p. 14
Other Non E. coli sRNAs	p. 15
Mechanisms: Antisense and Protein Sequestration	p. 15
Antisense: cis-Versus trans-Encoded	p. 16
Antisense: Sites of Action-Common Themes	p. 17
Antisense: Mechanisms of Inhibition-Common Themes?	p. 18
Antisense: Protein Helpers Required, And for What?	p. 19
Antisense: the Specificity Problem	p. 20
Concluding Remarks	p. 23
References	p. 25
Small Nucleolar RNAs: Identification, Structure, and Function	p. 31
Introduction	p. 31
Experimental Isolation of ncRNAs	p. 32
Specific Isolation	p. 32
General Isolation	p. 33
Computational Approaches to Find ncRNAs	p. 34
Small Nucleolar RNAs	p. 35
Box C/D snoRNAs	p. 37
Box H/ACA snoRNAs	p. 38
Small Cajal-Body-Specific RNAs	p. 40
Protein Association and Function	p. 41
Box C/D snoRNPs	p. 41
Box H/ACA snoRNPs	p. 42
Genomic Organization	p. 43
Modification Guide RNAs-Targets and Function	p. 45
Conclusion and Future Perspective	p. 46
References	p. 47
A Computational Approach to Search for Non-Coding RNAs in Large Genomic Data	p. 57
Introduction	p. 57
Probability of Patterns	p. 60
Design and Refinement of Patterns	p. 62
Searching Patterns in Large Sequence Sets	p. 68
WWW Tools	p. 70
References	p. 72
Experimental Strategies for the Identification and Validation of Target RNAs that Are Regulated by miRNAs	p. 75
Introduction	p. 76
History	p. 76
Biogenesis	p. 76
Computer Prediction	p. 78
Families of miRNAs	p. 78
Target Prediction by Data Base Search	p. 79
Genetic Identification	p. 79
Experimental Strategies for Target Identification	p. 79
Post-Transcriptional Inhibition of miRNA Function by Antisense Sequences	p. 80
Direct Identification of Target mRNA by a PCR Strategy Mimicking the miRNA Interaction	p. 84
Validation of miRNA/mRNA Target Pairs by Sensor Constructs	p. 85
Concluding Remarks	p. 87
References	p. 87
Protein Interactions with Double-Stranded RNA in Eukaryotic Cells	p. 91
Introduction	p. 91
Occurrence and Origin of Cellular Double-Stranded RNA	p. 92
Database Searches for Antisense RNA and Experimental Validation	p. 92
Structural Features of Double-Stranded RNA	p. 94
Protein Interactions	p. 96
Protein Domains Interacting with Double-Stranded RNA	p. 96
Molecular Architecture of dsRBD-Containing Proteins	p. 99
Cellular Response to Double-Stranded RNA	p. 107
Nuclear Processes	p. 107
Cytoplasmic Processes	p. 110
References	p. 111
Transitive and Systemic RNA Silencing: Both Involving an RNA Amplification Mechanism?	p. 119
Introduction	p. 119
RNA-Dependent RNA Polymerases and RNA Amplification	p. 121
RNA Amplification and Transitive Silencing	p. 122
Transitive Silencing in C. elegans	p. 122
Transitive Silencing in Plants	p. 124
Transitive Silencing in Fungi	p. 127
RNA Amplification and Systemic Silencing	p. 128
Systemic Silencing in Plants	p. 128
Systemic Silencing in C. elegans	p. 132
Absence of Transitive and Systemic RNA Silencing in Drosophila and Mammals	p. 133
References	p. 135
RNA Interference and Antisense Mediated Gene Silencing	p. 141
Introduction	p. 141
Parts of the RNAi Machine	p. 142
RNA-Directed RNA Polymerases	p. 144
Multicopy Enhancers of RNAi	p. 147
Inhibitors of Silencing	p. 147
Antisense RNA Mediated Gene Silencing	p. 149
Antisense RNA and RNAi	p. 151
Small Interfering RNAs	p. 151
RNA-Directed RNA Polymerases	p. 151
HelF	p. 152
Models	p. 152
References	p. 155
Epigenetic Silencing of Transposons in the Green Alga Chlamydomonas reinhardtii	p. 159
Introduction	p. 159
Post-Transcriptional Gene Silencing	p. 161
General Mechanisms	p. 161
PTGS and Transposon Silencing	p. 163
Transcriptional Gene Silencing	p. 167
General Mechanisms	p. 167
TGS and Transposon Silencing	p. 169
Concluding Remarks	p. 172
References	p. 172
RNA-Dependent Gene Silencing and Epigenetics in Animals	p. 179
MicroRNAs and Small Interfering RNAs-Two Different Types of Small RNAs	p. 179
Posttranscriptional RNAi	p. 181
Developmental Gene Regulation by miRNA-Mediated RNAi	p. 184
Epigenetic Gene Silencing	p. 186
Small dsRNAs May Mediate Epigenetic Silencing of Genes	p. 187
Epigenetic Silencing by Antisense Transcripts	p. 189
Dose Compensation on Sex Chromosomes	p. 191
The Role of roX RNAs in Dose Compensation in Drosophila	p. 191
X Chromosome Inactivation in Mammals	p. 192
Conclusions	p. 194
References	p. 195
Potentials of a Ribozyme-Based Gene Discovery System	p. 201
Introduction	p. 201
Randomized Ribozyme Libraries for Gene Discovery	p. 202
Identification of Genes Involved in Hepatitis C Virus Internal Ribosome Entry Site Mediated Translation	p. 205
Identification of Genes Involved in Cell Transformation	p. 205
Identification of Genes Involved in the Pathway of Apoptosis	p. 207
Identification of Metastasis-Related Genes	p. 208
Identification of Genes Involved in Alzheimer's Disease	p. 210
Conclusions	p. 211
References	p. 211
Subject Index	p. 217
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