Regulatory RNA

1. An Introduction to Regulatory RNA Motifs.- A Short Guide to the Book.- A Look Back: RNA, the Magic Molecule.- RNA Motifs in RNA Information Flow and RNA Catalysis.- Fig. l.1. Regulatory motifs in mRNA metabolism.- Fig.1.2. Two examples for RNA motifs (RRE, TAR).- Regulation of Gene Expression at the Level of the RNA.- Time or space dependent information release by RNA.- Catalysis and processing involving RNA.- Ribonucleoproteins: Combination of RNA and proteins.- RNA Motifs as a Tool to Look for Conserved Function.- Perspective: Context Specificity of RNA Within the Cell.- 2. Instances of Functional RNA (An Overview).- The Different Types of RNA.- Table 2.1. The different types of RNA (overview).- General Nuclear RNA Binding Motifs and Nucleoproteins.- RNA and RNA Motifs Involved in Splicing.- RNA-protein interactions; Fig. 2.1, rRNA.- Fig. 2.2, snRNAs.- Further variants: Selfsplicing introns.- Trans-splicing.- Editing.- Motifs and RNAs Involved in Ribosomal RNA Processing.- Post-Transcriptional Regulatory Signals in m-RNA.- 5? UTR.- Regulatory signals in the open reading frame.- Translation regulated by non-mRNA.- Modified residues in eukaryotic messenger mRNA.- Correction of missing stop codons by ioSa-RNA or tm-RNA.- The 3? UTR of Messenger RNA.- 3? UTR of mRNA (Fig. 2.3, LOX mRNA).- Fig. 2.4,3? processing motifs.- Direct Regulation of Gene Expression.- Autoregulatory RNA.- Antisense RNA.- Regulation of prokaryotic operons.- Cytoplasmic RNA and Motifs.- Ribozymes and Their Motifs.- Viral RNA.- Other RNA Species.- A Catalogue of Regulatory RNA.- Table 2.2 a) Well-characterized motifs.- Table 2.2 b) Complex motifs.- Figures of Specific Motifs.- Se-Cys-mRNA; Fig. 2.5 transferrin receptor mRNA.- Fig. 2.6, developmental RNA motifs.- 5? UTR of mRNA, Fig. 2.7, eukaryotic iron-responsive-elements.- Fig. 2.8, prokaryotic translational repression, ?-mRNA.- Correcting Mrna translation (Fig.2.9, 10Sa RNA/tmRNA).- Splicing Fig. 2.10, simple and.- Fig. 2.10b, detailed pathway.- Fig. 2.11, U6/U4 and U6/U2.- Fig. 2.11b, U5 loop.- Fig. 2.12, Ui/U6/U2/pre-mRNA.- Fig. 2.13, alternative splice site selection.- trans-splicing Fig. 2.14, leader-mRNAs and reaction.- Small nucleolar RNAs; Fig. 2.15.- Fig. 2.16, guide snoRNAs.- Viral RNAs (Fig. 2.17).- Antisense RNAs (Fig. 2.18, motifs;).- Fig. 2.19, RNA III.- Catalytic RNAs (Fig. 2.20, hammerhead; Fig. 2.21, hairpin).- RNAse P (Fig. 2.22, RNA cage).- Substrates in Fig. 2.23.- Selfsplicing introns (group I Fig. 2.24, group II Fig. 2.25) 66,.- Selfsplicing intron reactions (Fig. 2.26) 68,.- Cytoplasmic RNAs (Fig. 2.27, 7S RNA from SRP).- Many RNA Motifs Together: RNA Viridae.- Table 2.3 Classification of different RNA viridae.- Table 2.4 Important protein motifs recognizing RNA.- Protein Motifs Pointing to Interacting RNA Structures.- Modified Nucleotides.- Table 2.5 RNA modifications.- Perspective: From Known Instances to New Ones.- 3. Experimental Identification of New Functional RNA.- Typical Settings.- Revealing RNAs as Key Players in Cellular Regulation.- Double-stranded RNA in growth arrest.- Revealing regulatory structures in developmental RNAs.- Identification of further translational regulatory mRNA motifs.- Affinity screens to reveal RNA interaction with proteins.- Crosslinking to reveal RNA interaction with proteins.- Direct Confirmation of RNA Functionality.- Detailed probing of an RNA motif.- Revealing the exact RNA structure.- Finding RNA Motifs for a Desired Task.- RNA SELEX experiments.- Further approaches to design and engineer RNA.- Perspective: Future Directions.- Fig. 3.1 SELEX method and subsequent genomic search.- 4. Computer Based and Theoretical Identification of Regulatory RNA.- Steps Involved in an RNA Motif Search.- Describe the motif.- Identify common features.- Derive a consensus pattern.- From the analytical description to the search program.- Fig. 4.1 Consensus patterns.- Program tests.- Analyzing program output.- Comparing promising candidate structures and known examples.- Experimental and further tests for remaining best candidate.- A Typical Example.- Specific Motif Search Programs.- General Purpose Search Programs.- Evaluation of the Search Result.- The best candidate RNA structures.- Table 4.1. Reducing the number of RNA candidate structures.- Generalized Searches for RNA Motifs.- Table 4.2. Some points to check during an RNA motif search.- Perspective: An Incentive.- 5. Functional RNA Interactions.- Control of Information Release.- Catalysis.- Metabolism.- Evolution.- Protein-RNA Interactions.- Table 5.1. Examples of RNA specific protein interactions.- Modified Nucleotides in RNA.- Identification of modified nucleotides.- Modified nucleotides as tools to modulate RNA metabolism.- (Table 5.2. Some examples).- Dynamics.- Further Development.- Nanopatterns using oligonucleotides.- Artificial evolution of peptides coupled to UNA SELEX.- Medical Implications: Curing RNA by Trans-Splicing.- Medical Implications: Antisense Approaches.- Ribozyme mediated RNA repair (Fig.5.1).- Medical Implications: Ribozymes.- Hammerheads.- Medical Manipulation of Ribonucleoprotein Particles.- Targeting of RNA, Fig. 5.2.- Suggestions for Further Therapies.- Perspectives.- New targets.- Translational inhibition.- Understanding RNA tools.- 6. Areas of Research on Regulatory RNA and Functional RNA Motifs.- The Splicing of Messenger RNA.- Process and RNA recognition.- ATAC introns (Fig. 6.1).- Trans-Splicing.- RNA Editing.- Mammalian RNA editing.- Fig. 6.2 RNA editing examples.- Editing in trypanosomes.- in slime-mold physarum.- in plant mitochondria and chloroplasts.- in hepatitis delta virus.- Ribosomal RNA Processing and Ribosome Biogenesis.- A focus of interest.- Ribosomal RNA processing steps.- Pathway (Fig. 6.3).- snoRNAs.- Nuclear RNA Transport.- Messenger RNA and Regulatory Motifs: The 5? Untranslated Region in mRNA.- Open Reading Frames in mRNA.- Is a cDNA sequence complete?.- Regulation of ORF translation by transfer-RNA redundancy.- The 3? Untranslated Region in mRNA.- 3? UTR in parasites.- Se-Cys mRNAs.- Motif searches and a SELEX approach.- Detailed analysis of a complex RNA stability motif in the 3? UTR.- Polyadenylation signals.- Developmental differentiation signals in the 3? UTR.- Three hybrid screening system (Fig. 6.4).- Developmental localization signals in the 3? UTR.- Catalytic RNAs.- Selfsplicing introns.- Viral RNAs.- Perspective: New Interesting RNA Structures.- Cytoplasmic RNAs.- XIST, (X chromosome inactivation) RNA.- H19 RNA and imprinting.- C. elegans lin-4 RNA.- Telomerases: maintaining the ends of the chromosomes.- Fig. 6.5. Telomerase RNA and telomers.- Small RNAs in E. coli.- OxyS (Fig. 6.6).- 7. Future Research.- Splicing.- Editing, Trans-Splicing and Beyond.- Ribosomal RNA and Cofactors.- Signals in the mRNA.- Antisense RNA.- Biotechnological Applications.- Conclusion.- Alphabetical References.