ISBN: 354041701X
TITLE: RNA Motifs and Regulatory Elements
AUTHOR: Dandekar (Ed.)
TOC:

1. Introduction 1
1.1 Book Overview 1
1.2 RNA, the Underestimated Molecule 1
1.3 Examining Regulatory RNA Elements 3
1.4 Regulation of Gene Expression 7
1.5 Catalytic Active RNA 8
1.6 Combination of RNA and Proteins 9
1.7 RNA Motifs and Elements Indicate Conserved Function 9
1.8 Context Specificity of RNA Within the Cell 10
2. Instances of Functional RNA 13
2.1 Overview 13
2.2 The Different Types of RNA and Their Regulatory Elements 15
2.3 RNA Motifs Involved in Splicing 20
2.4 RNA Editing 22
2.5 Posttranscriptional Regulatory Signals in mRNA 23
2.6 Further Regulatory RNAs 26
2.7 Modified Residues in Eukaryotic mRNAs 26
2.8 Correction of Missing Stop Codons by 10Sa-RNA 27
2.9 Direct Regulation of Gene Expression 27
2.10 Regulation of Prokaryotic Operons 28
2.11 Cytoplasmic RNA Motifs 29
2.12 Ribozymes and Their Motifs 30
2.13 Viral RNA 30
2.14 Other RNA Species 32
2.15 A Catalogue of Regulatory RNA Motifs 33
2.16 RNA Motifs in RNA Viridae 40
2.17 Protein Motifs Pointing to Interacting RNA Structures 42
2.18 Modified Nucleotides 43
2.19 Perspective: from Known Instances to New Ones 44
2.20 An Atlas of Regulatory RNA Elements 44
3. Experimental Identification of New Functional RNA 69
3.1 Introduction 69
3.2 Typical Challenges 70
3.3 Cellular Regulation 72
3.4 Confirmation of RNA Functionality 77
4. Computer-Based and Theoretical Identification of Regulatory RNA 85
4.1 Introduction 85
4.2 Carrying Out an RNA Motif Search 86
4.3 Example Searches 92
4.4 Motif Specific Searches for RNA Elements 93
4.5 General-Purpose Search Programs 98
4.6 Evaluation of the Search Result 102
5. Functional RNA Interactions 111
5.1 Introduction 111
5.2 Cellular Information Transfer from mRNA 111
5.3 Catalytic RNA 114
5.4 RNA Motif Evolution 117
5.5 RNA-Protein Interactions 118
5.6 Designing Interactions 123
5.7 Medical Implications 126
5.8 Perspectives 135
6 Areas of Research on RNA Motifs and Regulatory Elements 139
6.1 Introduction 139
6.2 The Transcription of DNA 139
6.3 The Splicing of Messenger RNA 140
4.4 Trans-Splicing 144
6.5 RNA Editing 147
6.6 Ribosomal RNA Processing Steps 154
6.7 Nuclear RNA Transport 158
6.8 Regulatory Motifs in mRNA 159
6.9 Posttranscriptional Gene Silencing and RNA Interference 166
6.10 Catalytic RNA and Motifs 168
6.11 Viral RNAs 170
7. Outlook 181
7.1 New Types and Classes of Regulatory RNAs Come up at an Unprecedented Pace 181
7.2 Established Areas of Research 182
7.3 Conclusion 184
8. Figure-Acknowledgement 185
9. References 187
10. Subject Index 225
END
