This book provides an introduction to and an overview of the field of regulatory RNA, focusing on the identification of regulatory elements and motifs in such RNA molecules. Central to the book is the use of appropriate techniques to identify regulatory RNA and regulatory motifs. The prospects for this new and expanding research field - understanding regulatory RNA elements and motifs - are also explored, including new developments, medical applications, and applications in other fields.

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.- Regulation of Gene Expression at the Level of the RNA.- 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.- General Nuclear RNA Binding Motifs and Nucleoproteins.- RNA and RNA Motifs Involved in Splicing.- Motifs and RNAs Involved in Ribosomal RNA Processing.- Post-Transcriptional Regulatory Signals in m-RNA.- Direct Regulation of Gene Expression.- Cytoplasmic RNA and Motifs.- Ribozymes and Their Motifs.- Viral RNA.- Other RNA Species.- A Catalogue of Regulatory RNA.- Figures of Specific Motifs.- Many RNA Motifs Together: RNA Viridae.- Protein Motifs Pointing to Interacting RNA Structures.- Modified Nucleotides.- Perspective: From Known Instances to New Ones.- 3. Experimental Identification of New Functional RNA.- Typical Settings.- Revealing RNAs as Key Players in Cellular Regulation.- Direct Confirmation of RNA Functionality.- Finding RNA Motifs for a Desired Task.- Perspective: Future Directions.- 4. Computer Based and Theoretical Identification of Regulatory RNA.- Steps Involved in an RNA Motif Search.- A Typical Example.- Specific Motif Search Programs.- General Purpose Search Programs.- Evaluation of the Search Result.- Generalized Searches for RNA Motifs.- Perspective: An Incentive.- 5. Functional RNA Interactions.- Control of Information Release.- Catalysis.- Metabolism.- Evolution.- Protein-RNA Interactions.- Modified Nucleotides in RNA.- Dynamics.- Further Development.- Medical Implications: Curing RNA by Trans-Splicing.- Medical Implications: AntisenseApproaches.- Medical Implications: Ribozymes.- Medical Manipulation of Ribonucleoprotein Particles.- Suggestions for Further Therapies.- Perspectives.- 6. Areas of Research on Regulatory RNA and Functional RNA Motifs.- The Splicing of Messenger RNA.- Trans-Splicing.- RNA Editing.- Ribosomal RNA Processing and Ribosome Biogenesis.- Nuclear RNA Transport.- Messenger RNA and Regulatory Motifs: The 5? Untranslated Region in mRNA.- Open Reading Frames in mRNA.- The 3? Untranslated Region in mRNA.- Catalytic RNAs.- Viral RNAs.- Perspective: New Interesting RNA Structures.- 7. Future Research.- Splicing.- Editing, Trans-Splicing and Beyond.- Ribosomal RNA and Cofactors.- Signals in the mRNA.- Antisense RNA.- Biotechnological Applications.- Conclusion.- Alphabetical References.