1 THE RNA INFRASTRUCTURE: AN INTRODUCTION TO ncRNA NETWORKS .... 1
Lesley J. Collins
Abstract ..................................................... 1
Introduction ................................................. 1
RNAs Processing Other RNAs ................................... 2
Spatial Regulation of Eukaryotic RNA Processing .............. 7
RNA Regulation, Connecting Components of the RNA-
Infrastructure ............................................... 9
Conclusion .................................................. 15
2 RNA INTERACTIONS ............................................ 20
Manja Marz and Peter F. Stadler
Abstract .................................................... 20
Introduction ................................................ 20
ncRNA-DNA Interactions ...................................... 21
RNA-RNA Interactions ........................................ 23
ncRNA-Protein Interactions .................................. 31
Conclusion .................................................. 33
3 PLANT RNA SILENCING IN VIRAL DEFENCE ........................ 39
Vitantonio Pantaleo
Abstract .................................................... 39
Introduction ................................................ 39
Generation of Viral Small Interfering RNAs: Viruses,
vsiRNAs and Dicers .......................................... 40
Post-Dicing Modification of vsiRNAs ......................... 47
Antiviral Effector Complexes ................................ 47
Amplification and Spread of Antiviral Defence ............... 49
Movement of Antiviral Silencing ............................. 51
Viral Suppressors of RNA Silencing .......................... 52
Conclusion .................................................. 53
4 MicroRNAS AS POST-TRANSCRIPTIONAL MACHINES AND THEIR
INTERPLAY WITH CELLULAR NETWORKS ............................ 59
Sarath Chandra Janga and Swathi Vallabhaneni
Abstract .................................................... 59
Introduction ................................................ 60
Biogenesis, Genomic Organization and Evolution of miRNAs .... 61
Methods to Identify miRNAs and Their Targets ................ 63
MicroRNA Interplay with Other Cellular Networks ............. 65
Expression Dynamics and Crosstalk of miRNAs with Other
Regulatory Factors .......................................... 69
Conclusion .................................................. 70
5 SPATIOTEMPORAL ASPECTS OF MicroRNA-MEDIATED GENE
REGULATION .................................................. 75
Joris Pothof and Dik C. van Gent
Abstract .................................................... 75
Introduction ................................................ 75
DNA Damage Response as an Example of Multilayered
Regulation .................................................. 77
MicroRNA-Mediated Gene Silencing in the DDR ................. 78
Mechanism of Fast MicroRNA Regulation ....................... 81
Localization of the MicroRNA-Mediated Gene Silencing
Machinery ................................................... 82
Conclusion .................................................. 84
6 SPLICEOSOMAL RNA INFRASTRUCTURE: THE NETWORK OF SPLICING
COMPONENTS AND THEIR REGULATION BY miRNAS ................... 86
Lesley J. Collins
Abstract .................................................... 86
Introduction ................................................ 86
The Spliceosome as an Example of the RNA-Infrastructure ..... 87
RNA-Protein Interaction Networks ............................ 89
Regulatory (Expression Modulated) Networks .................. 93
Spatiotemporal Dynamic RNA Networks ......................... 98
Conclusion ................................................. 100
7 CONSTRUCTION, STRUCTURE AND DYNAMICS OF POST-
TRANSCRIPTIONAL REGULATORY NETWORK DIRECTED BY RNA-
BINDING PROTEINS ........................................... 103
Sarath Chandra Janga and Nitish Mittal
Abstract ................................................... 103
Introduction ............................................... 104
RNA Binding Proteins and Post-Transcriptional Regulation ... 104
Methods to Identify RBPs and Their Targets ................. 107
RBPs and Post-Transcriptional Operons ...................... 109
Post-Transcriptional Network Formed by RBPs ................ 110
Expression Dynamics of RBPs in Post-Transcriptional
Networks ................................................... 112
Conclusion ................................................. 114
8 SAFE KEEPING THE MESSAGE: mRNP COMPLEXES TWEAKING AFTER
TRANSCRIPTION .............................................. 118
Said Hafidh, Věra Čapková and David Honys
Abstract ................................................... 118
Introduction ............................................... 119
RNP-Infrastructure; Post-Transcriptional Modulator of
Gene Expression ............................................ 119
Pre-mRNA Processing and the Initiation of mRNP Formation ... 122
Mobilization to the Site of Storage and niRNA
Localization ............................................... 125
Cytoskeleton: Actin and Microtubule Dynamics as
a Floating Raft for mRNPs Subcellular Localization ......... 126
Intra- and Intercellular Translocation of mRNPs ............ 126
Storage of mRNPs and mRNA Turnover ......................... 127
Systematic Translation Repression by Small RNAs ............ 131
Reinitiating Translation of the Localized,
Translationally Sequestered mRNAs .......................... 132
Conclusion ................................................. 133
9 UNEXPECTED FUNCTIONS OF tRNA AND tRNA PROCESSING ENZYMES ... 137
Rebecca L. Hurto
Abstract ................................................... 137
Introduction ............................................... 137
tRNAs and Transcription .................................... 138
tRNA Fragments ............................................. 140
Aminoacyl-tRNA Functions Beyond Translation ................ 147
tRNA Processing Enzymes Affect More Than tRNA .............. 148
Aminoacyl-tRNA Synthetases, tRNA and Disease ............... 149
Conclusion ................................................. 151
10 PROGRAMMED DNA ELIMINATION IN TETRAHYMENA: A SMALL RNA-
MEDIATED GENOME SURVEILLANCE MECHANISM ..................... 156
Kensuke Kataoka and Kazufumi Mochizuki
Abstract ................................................... 156
Introduction ............................................... 157
Nuclear Dimorphism in Tetrahymena .......................... 159
Epigenetic Regulation of DNA Elimination by Small RNAS ..... 163
Biogenesis of scnRNA ....................................... 163
scnRNA Selection ........................................... 165
scnRNA-Induced Heterochromatin Formation and DNA
Elimination ................................................ 166
Evolutionary Considerations ................................ 167
Future Prospects ........................................... 169
Conclusion ................................................. 170
11 LONG NONCODING RNA AND EPIGENOMICS ......................... 174
Chandrasekhar Kanduri
Abstract ................................................... 174
Introduction ............................................... 174
Long ncRNAs and Tumor Suppressor Genes ..................... 176
Long ncRNAs and Homeobox Genes ............................. 177
Long ncRNAs and Dosage Compensation ........................ 179
Long ncRNAs and Pluripotency ............................... 184
Long ncRNAs and Genomic Imprinting ......................... 186
Long ncRNAs and Centromeric Heterochromatin ................ 189
Conclusion ................................................. 191
12 PROMOTER-ASSOCIATED LONG NONCODING RNAs REPRESS
TRANSCRIPTION THROUGH A RNA BINDING PROTEIN TLS ............ 196
Riki Kurokawa
Abstract ................................................... 196
Introduction ............................................... 197
The Target RNA Sequences Recognized by TLS ................. 197
Domain Structure of TLS .................................... 200
Transcription-Regulatory Long ncRNA, Cyclin Dl pncRNA ...... 203
Conclusion ................................................. 206
13 RNA NETWORKS IN PROKARYOTES I: CRISPRs AND RIBOSWITCHES .... 209
Patrick J. Biggs and Lesley J. Collins
Abstract ................................................... 209
Introduction ............................................... 209
Riboswitches Control Gene and Operon Expression Via
Metabolite Binding ......................................... 210
The CRISPR/Cas System is Analogous, but Not Homologous,
to Eukaryotic RNAi ......................................... 213
Conclusion ................................................. 218
14 RNA NETWORKS IN PROKARYOTES II: tRNA PROCESSING AND SMALL
RNAs ....................................................... 221
Lesley J. Collins and Patrick J. Biggs
Abstract ................................................... 221
Introduction ............................................... 221
RNase P and tRNA Processing in Bacteria and Archaea ........ 222
Bacterial Small RNAs and Sigma Factors ..................... 224
Transfer Messenger RNA V ................................... 227
Conclusion ................................................. 228
15 LOCALIZATION OF THE BACTERIAL RNA INFRASTRUCTURE
Kenneth C. Keiler
Abstract ................................................... 231
Introduction ............................................... 231
Localized Transcription and mRNA ........................... 232
Spatial Control of RNA Degradation and Processing .......... 233
EF-Tu is a Component of the Cytoskeleton ................... 235
Localization of Trans-Translation Components ............... 235
Spatial Control of Gene Expression ......................... 236
Conclusion ................................................. 236
16 SMALL RNA DISCOVERY AND CHARACTERISATION IN EUKARYOTES
USING HIGH-THROUGHPUT APPROACHES ........................... 239
Helio Pais, Simon Moxon, Tamas Dalmay and Vincent Moulton
Abstract ................................................... 239
Introduction ............................................... 239
The Mechanisms of RNA Silencing ............................ 240
Using Microarrays and DNA Sequencing to Measure RNA ........ 243
High-Throughput Approaches for the Discovery and
Functional Classification of sRNAs ......................... 244
Conclusion ................................................. 250
17 HOW OLD ARE RNA NETWORKS? .................................. 255
Toni Daly, X. Sylvia Chen and David Penny
Abstract ................................................... 255
Introduction ............................................... 255
Regulatory Networks of Small RNAs .......................... 256
RNA Regulation and Defence Against the Dark Arts ........... 259
Other Regulatory RNAs ...................................... 266
How Old are the Different Interactions of RNA? ............. 267
Conclusion ................................................. 269
INDEX ......................................................... 275
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