RNA Infrastructure and Networks

Transcription

1 RNA Infrastructure and Networks Edited by Lesley J. Collins Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand volume e contact Springer Science+Business Media, LLC Landes Bioscience

2 CONTENTS 1. THE RNA INFRASTRUCTURE: AN INTRODUCTION TO ncrna NETWORKS... l Lesley J. Collins Abstract... I Introduction... l RNAs Processing Other RNAs... 2 Spatial Regulation ofeukaryotic RNA Processing... 7 RNA Regulation, Connecting Components of the RNA-Infrastructure... 9 Conclusion RNA INTERACTIONS Manja Marz and Peter F. Stadler Abstract Introduction ncrna-dna Interactions RNA-RNA Interactions ncrna-protein Interactions Conclusion PLANT RNA SILENCING IN VIRAL DEFENCE Vitantonio Pantaleo Abstract Introduction... m 39 Generation of Viral Small Interfering RNAs: Viruses, vsirnas and Dicers Post-Dicing Modification of vsirnas Antiviral Effector Complexes Amplification and Spread of Antiviral Defence Movement of Antiviral Silencing Viral Suppressors of RNA Silencing Conclusion XV

3 xvi CONTENTS 4. MicroRNAS AS POST-TRANSCRIPTIONAL MACHINES AND THEIR INTERPLAY WITH CELLULAR NETWORKS Sarath Chandra Janga and Swathi Vallabhaneni Abstract Introduction Biogenesis, Genomic Organization and Evolution of mirnas Methods to Identify mirnas and Their Targets MicroRNA Interplay with Other Cellular Networks Expression Dynamics and Crosstalk of mirnas with Other Regulatory Factors Ct~nclusion SPATIOTEMPORALASPECTS OF MicroRNA-MEDIATED GENE REGULATION Joris Pothof and Dik C. van Gent Abstract Introduction DNA Damage Response as an Example of Multilayered Regulation MicroRNA-Mediated Gene Silencing in the DDR Mechanism of Fast MicroRNA Regulation Localization of the MicroRNA-Mediated Gene Silencing Machinery Conclusion SPLICEOSOMAL RNA INFRASTRUCTURE: THE NETWORK OF SPLICING COMPONENTS AND THEIR REGULATION BY mirnas Lesley J. Collins Abstract Introduction The Spliceosome as an Example of the RNA-Infrastructure RNA-Protein Interaction Networks Regulatory (Expression Modulated) Networks Spatiotemporal Dynamic RNA Networks Conclusion CONSTRUCTION, STRUCTURE AND DYNAMICS OF POST-TRANSCRIPTIONAL REGULATORY NETWORK DIRECTED BY RNA-BINDING PROTEINS Sarath Chandra Janga and Nitish Mittal Abstract Introduction RNA Binding Proteins and Post-Transcriptional Regulation Methods to Identify RBPs and Their Targets RBPs and Post-Transcriptional Operons Post-Transcriptional Network Formed by RBPs

4 CONTENTS contents xvii Expression Dynamics ofrbps in Post-Transcriptional Networks Conclusion s. SAFE KEEPING THE MESSAGE: mrnp COMPLEXES TWEAKING AFTER TRANSCRIPTION Said Hafidh, Vera Capkova and David Honys Abstract Introduction RNP-Infrastructure; Post-Transcriptional Modulator of Gene Ex pre sion Pre-mRNA Processing and the Initiation of mrnp Formation Mobilization to the Site of Storage and mrna Localization Cyto keleton: Actin and M icrotubule Dynamics as a Floating Raft for mrnp Subcellular Localization Intra- and Intercellular Translocation of mrnps Storage of mrnps and mrna Turnover Systematic Translation Repression by Small RNAs Reinitiating Translation of the Localized, 1'ranslationally Sequestered mrnas Conclusion UNEXPECTED FUNCTIONS OF trnaand trna PROCESSING ENZYMES Rebecca L. Hurto Abstract Introduction trnas and Transcription trna Fragments AminoacyJ-tRNA Functions Beyond Translation trna Processing Enzymes Affect More Than trna Aminoacyl-tRNA Synthetases, trna and Disease Conclusion PROGRAMMED DNA ELIMINATION IN TETRAHYMENA: A SMALL RNA-MEDIATED GENOME SURVEILLANCE MECHANISM Kensuke Kataoka and Kazufumi Mochizuki Abstract Introduction... l57 NucJear Dimorphism in Tetrahymena Epigenetic Regulation of DNA Elimination by Small RNAS Biogenesis of scnrna scnrna Selection scnrna-induced Heterochromatin Formation and DNA Elimination Evolutionary Considerations Future Prospects Conclusion

5 xviii CONTENTS 11. LONG NONCODING RNAAND EPIGENOMICS Chandrasekhar Kanduri Abstract lntroduction Long ncrnas and Thmor Suppressor Genes Long ncrnas and Homeobox Genes Long ncrnas and Dosage Compensation Long ncrnas and Pluripotency Long ncrnas and Genomic Imprinting Long ncrnas and Centromeric Heterochromatin Conclusion PROMOTER-ASSOCIATED LONG NON CODING RNAs REPRESS TRANSCRIPTION THROUGH A RNA BINDING PROTEIN TLS Riki Kurokawa Abstract Jntroduction The Target RNA Sequences Recognized by TLS Domain Structure of TLS Transcription-Regulatory Long ncrna, Cyclin D1 pncrna Conclusion RNA NETWORKS IN PROKARYOTES I: CRISPRs AND RIBOSWITCHES Patrick J. Biggs and Lesley J. Collins Abstract Introduction Riboswitcbes Control Gene and Operon Expression Via Metabolite Binding The CRJSPR!Cas System is Analogous, but Not Homologous, to Eukaryotic RNAi Conclusion RNA NETWORKS IN PROKARYOTES II: trna PROCESSING AND SMALL RNAs Lesley J. Collins and Patrick J. Biggs Abstract Introduction RNase P and trna Processing in Bacteria and Arcbaea Bacterial Small RNAs and Sigma Factors Transfer Messenger RNA Conclu ion

6 CONTENTS Ai contents OCALIZATION OF THE BACTERIAL RNA INFRASTRUCTURE L Kenneth c. Keiler AbS t Til Ct... Introduction...:...: L rzed Trao er1ption and mrna ;~~~ Control of RNA Degradation and Processing EF Tu is a Component of the C::ytoskeleton Localization of Trans-Translatio? Components pari a I Control of Gene "ExpressiOn Conclusion SMALL RNA DISCOVERY AND CHARACTERISATION IN EUKARYOTES USING HIGH-THROUGHPUT APPROACHES Helio Pais, Simon Moxon, Tamas Dalmay and Vincent Moulton Abstract Introduction The Mechanisms of RNA Silencing Using Microarrays and DNA Sequencing to Measure RNA High-Throughput Approaches for the Discovery and Functional Classification of srnas Conclusion HOW OLD ARE RNA NETWORKS? Toni Daly, X. Sylvia Chen and David Penny Abstract Introduction Regulatory Networks of Small RNAs RNA Regulation and Defence Against the Dark Arts Other Regulatory RNAs How Old are the Different Interactions of RNA? Conclusion INDEX xix