Rna Motifs and Regulatory Elements

by Dandekar, Thomas; Bengert, P.

• ISBN13: 9783540417019
• ISBN10: 354041701X
• Edition: 2nd
• Format: Hardcover
• Copyright: 2002-01-01
• Publisher: Springer Verlag

Summary

RNA Motifs and Regulatory Elementsis the new edition of the successful book, "Regulatory RNA". It alerts the reader to the importance of regulatory RNA elements for the many different areas of cellular life. The computational and experimental methods and tools to search for new interesting regulatory RNA structures are explained and compared. The knowledge on regulatory RNA structures and elements already available is concisely summarized as well as catalogued. In addition, interesting RNA elements are analyzed in detail regarding their dynamics, regulation, and as a dominant topic of current resarch in molecular biology, including areas such as RNA mediated regulation of gene-expression, DNA/RNA chip data, and ribozymes, splicing, or telomerases in aging. Medical implications are also covered. Future progress and research are finally outlined.

Table of Contents

Introduction	p. 1
Book Overview	p. 1
RNA, the Underestimated Molecule	p. 1
Examining Regulatory RNA Elements	p. 3
Regulation of Gene Expression	p. 7
Catalytic Active RNA	p. 8
Combination of RNA and Proteins	p. 9
RNA Motifs and Elements Indicate Conserved Function	p. 9
Context Specificity of RNA Within the Cell	p. 10
Instances of Functional RNA	p. 13
Overview	p. 13
The Different Types of RNA and Their Regulatory Elements	p. 15
RNA Motifs Involved in Splicing	p. 20
RNA Editing	p. 22
Posttranscriptional Regulatory Signals in mRNAt	p. 23
Further Regulatory RNAs	p. 26
Modified Residues in Eukaryotic mRNAs	p. 26
Correction of Missing Stop Codons by lOSa-RNA	p. 27
Direct Regulation of Gene Expression	p. 27
Regulation of Prokaryotic Operons	p. 28
Cytoplasmic RNA Motifs	p. 29
Ribozymes and Their Motifs	p. 30
Viral RNA	p. 30
Other RNA Species	p. 32
A Catalogue of Regulatory RNA Motifs	p. 33
RNA Motifs in RNA Viridae	p. 40
Protein Motifs Pointing to Interacting RNA Structures	p. 42
Modified Nucleotides	p. 43
Perspective: from Known Instances to New Ones	p. 44
An Atlas of Regulatory RNA Elements	p. 44
Experimental Identification of New Functional RNA	p. 69
Introduction	p. 69
Typical Challenges	p. 70
Cellular Regulation	p. 72
Confirmation of RNA Functionality	p. 77
Computer-Based and Theoretical Identification of Regulatory RNA...	p. 85
Introduction	p. 85
Carrying Out an RNA Motif Search	p. 86
Example Searches	p. 92
Motif Specific Searches for RNA Elements	p. 93
General-Purpose Search Programs	p. 98
Evaluation of the Search Result	p. 102
Functional RNA Interactions	p. 1ll
Introduction	p. 111
Cellular Information Transfer from mRNA	p. 111
Catalytic RNA	p. 114
RNA Motif Evolution	p. 117
RNA-Protein Interactions	p. 118
Designing Interactions	p. 123
Medical Implications	p. 126
Perspectives	p. 135
Areas of Research on RNA Motifs and Regulatory Elements	p. 139
Introduction	p. 139
The Transcription of DNA	p. 139
The Splicing of Messenger RNA	p. 140
Tans-Splicing	p. 144
RNA Editing	p. 147
Ribosomal RNA Processing Steps	p. 154
Nuclear RNA Transport	p. 158
Regulatory Motifs in mRNA	p. 159
Posttranscriptional Gene Silencing and RNA Interference	p. 166
Catalyic RNA and Motifs	p. 168
Viral RNAs	p. 170
Outlook	p. 181
New Types and Classes of Regulatory RNAs Come up at an Unprecedented Pace	p. 181
Established Areas of Research	p. 182
Conclusion	p. 184
Figure-Acknowledgement	p. 185
References	p. 187
Subject Index	p. 225
Table of Contents provided by Publisher. All Rights Reserved.