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RNA Biology

ISBN: 978-3-527-32278-7
380 pages
May 2011
RNA Biology (3527322787) cover image
Written with biologists, biochemists and other molecular scientists in mind, this volume meets the long-felt need for a textbook dedicated to the topic and recreates the excitement surrounding the scientific revolution sparked by the discovery of RNA interference in 1998. Students and instructors alike will profit from the author's exclusive first-hand knowledge, drawing on his breakthrough discoveries at the Tuschl lab at Rockefeller University.
Gunter Meister abandons the traditionalist treatment of nucleic acids found in most biochemistry and molecular biology texts, adopting instead a modern approach in both concept and scope. The text is divided into three parts, on mRNA, non-coding RNA, and RNomics, and the author addresses the traditional roles of RNA in the transmission and regulation of genetic information, as well as the recently discovered functions of small RNA species in pathogen defense, cell differentiation and higher-level genomic regulation.
All set to become the standard for teaching molecular science to biologists and biochemists.
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Preface.

Part One mRNA Biology.

1 Introduction.

1.1 RNA Building Blocks.

1.2 RNA Folding.

1.3 The RNA World Hypothesis.

1.4 Functions of RNA.

1.5 Protein Classes that are Required for RNA Function.

References.

2 Transcription of Pre-mRNAs.

2.1 Structure and Organization of Protein Coding Genes.

2.2 Transcription of mRNAs by RNA Polymerase II.

2.3 Transcriptional Termination of Pre-mRNAs.

2.4 Transcription is Coupled to Other mRNA Maturation Steps.

2.5 Summary.

References.

3 Capping of the Pre-mRNA 5´ End.

3.1 m7G-cap Structure.

3.2 mRNA Capping Enzymes.

3.3 5´ Capping is Coupled to Transcription.

3.4 5´ Cap Binding Proteins.

3.5 Summary.

References.

4 3´ End Processing of Pre-mRNAs.

4.1 Polyadenylation Signals.

4.2 Proteins Involved in 3´ End Processing of Pre-mRNAs.

4.3 30 End Processing is Tightly Linked to Transcriptional Termination.

4.4 Alternative Polyadenylation.

4.5 Cytoplasmic Polyadenylation.

4.6 3´ End Processing of Histone mRNAs.

4.7 Summary.

References.

5 Splicing of Eukaryotic Pre-mRNAs.

5.1 Group I, II and III Introns.

5.2 The Mechanism of pre-mRNA Splicing.

5.3 The Spliceosome.

5.4 The U12-Dependent Minor Spliceosome.

5.5 Coupling of Splicing with Transcription and 5´ Capping.

5.6 Alternative Splicing and the Complexity of Genomes.

5.7 Summary.

5.8 Questions.

References.

6 mRNA Export from the Nucleus to the Cytoplasm.

6.1 Nuclear Import and Nuclear Export.

6.2 mRNA Export Receptors.

6.3 Adaptors that Bridge mRNAs with Export Receptors.

6.4 Mechanism of mRNA Export.

6.5 Coupling of mRNP Export to Other Steps of mRNA Maturation.

6.6 Summary.

6.7 Questions.

References.

7 Translation.

7.1 Amino Acids, mRNAs, tRNAs.

7.2 The Ribosome.

7.3 The Mechanisms of Translation.

7.4 Translational Regulation.

7.5 Coupling Translation with Other mRNA Maturation and Quality Control Steps.

7.6 Summary.

7.7 Questions.

References.

8 Deadenylation of mRNA.

8.1 Deadenylating Enzymes.

8.2 Summary.

8.3 Questions.

References.

9 mRNA Decapping.

9.1 Decapping Enzymes are the Core of the mRNA Decapping Machinery.

9.2 Scavenger Decapping Enzyme DcpS.

9.3 Regulation of mRNA Decapping.

9.4 Intracellular Localization of mRNA Decapping.

9.5 Summary.

9.6 Questions.

References.

10 mRNA Decay Pathways.

10.1 Deadenylation-Dependent mRNA Decay.

10.2 Deadenylation-Independent mRNA Decay.

10.3 Endoribonuclease-Mediated mRNA Decay.

10.4 Regulation of mRNA Decay.

10.5 RNA Degradation in Bacteria.

10.6 Summary.

10.7 Questions.

References.

11 mRNA Quality Control.

11.1 Nuclear mRNA Quality Control Mechanisms.

11.2 Nonsense-Mediated mRNA Decay (NMD).

11.3 Other mRNA Quality Control Pathways.

11.4 Summary.

11.5 Questions.

References.

Part Two Non-Coding RNA Biology.

12 Ribosomal RNAs and the Biogenesis of Ribosomes.

12.1 Genomic Organization of Ribosomal RNA Genes.

12.1.1 Bacteria and Archaea.

12.2 Transcription of Ribosomal RNA Genes.

12.3 Maturation of rRNAs.

12.4 Assembly of Ribosomal Subunits.

12.5 Nuclear Export of Ribosomal Subunits.

12.6 Modification, Structure and Function of rRNAs.

12.7 Summary.

12.8 Questions.

References.

13 Transfer RNAs.

13.1 Genomic Organization and Transcription of tRNA Genes.

13.2 Processing to Mature tRNAs.

13.3 tRNA Modifications.

13.4 Nuclear Export of tRNAs.

13.5 Tertiary Structure of tRNAs.

13.6 Summary.

References.

14 The 7SL RNA and the Signal Recognition Particle.

14.1 Architecture of the SRP.

14.2 SRP-Mediated Protein Translocation.

14.3 Summary.

References.

15 Regulation of Transcription: the 7SK Small Nuclear RNA.

15.1 Architecture of the 7SK snRNA.

15.2 The 7SK snRNP Functions as Transcriptional Regulator.

15.3 Other Small Non-Coding RNAs that Interfere with Transcription.

15.4 Summary.

References.

16 Small Nucleolar RNAs.

16.1 Genomic Organization and snoRNA Transcription.

16.2 Box H/ACA snoRNAs.

16.3 Box C/D snoRNAs.

16.4 Maturation of Functional snoRNPs.

16.5 Orphan snoRNAs.

16.6 The Telomerase RNP.

16.7 Summary.

References.

17 Spliceosomal Small Nuclear RNAs.

17.1 Transcription and Maturation of Spliceosomal snRNAs.

17.2 The Structure of UsnRNPs.

17.3 Assembly of Spliceosomal snRNPs.

17.4 Summary.

17.5 Questions.

References.

18 Small Non-Coding RNAs and the Mechanism of Gene Silencing.

18.1 Short Interfering RNAs and the Mechanism of RNA Interference.

18.2 Dicer.

18.3 RNA-Dependent RNA Polymerases.

18.4 Argonaute Proteins.

18.5 microRNAs and the Regulation of Gene Expression.

18.6 PiRNAs and the Regulation of Mobile Genetic Elements in the Germ Line.

18.7 Small RNAs with Functions in Chromatin Regulation.

18.8 The CRISPR System – A Bacterial and Archaeal Defense Mechanism.

18.9 Summary.

References.

19 Long Non-Coding RNAs.

19.1 The XIST Non-Coding RNA and X Chromosome Inactivation.

19.2 Dosage Compensation in Flies.

19.3 Non-Coding RNAs and the Regulation of Imprinting.

19.4 The Regulation of HOX Genes by Long Non-Coding RNAs.

19.5 Long non-Coding RNAs are Common in Complex Genomes.

19.6 Summary.

References.

20 RNA Editing.

20.1 RNA Editing by U Insertions or Deletions.

20.2 RNA Editing by Base Modification.

20.3 Summary.

References.

21 Ribozymes Catalytic RNA Molecules.

21.1 Identification of Catalytic RNAs.

21.2 Mechanisms and Secondary Structures of Different Ribozymes.

21.3 Summary.

References.

22 Riboswitches and RNA Sensors.

22.1 Mechanisms of Riboswitch Function.

22.2 Riboswitch Structures.

22.3 RNA Thermometers.

22.4 Summary.

References.

23 RNomics.

23.1 ‘‘Omics’’ Approaches.

23.2 Experimental RNA Profiling Strategies.

23.3 RNA Biology and the Complexity of Genomes.

23.4 Summary.

References.

Appendix: Answers to Questions.

Index.

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Gunter Meister is the head of the department of biochemistry I of the University of Regensburg, Germany. He obtained his PhD degree from the University of Munich and the Max-Planck-Institute of Biochemistry, working on RNA-protein complexes. Thereafter, he joined the group of Tom Tuschl at the Rockefeller University in New York (USA), where he worked on RNA interference and small non-coding RNAs. After his postdoctoral time in New York, he went back to the Max-Planck-Institute of Biochemistry as independent group leader and head of the "RNA Biology" group. Gunter Meister has received an EMBO long-term fellowship as well as an Emmy Noether fellowship from the Deutsche Forschungsgemeinschaft. He was awarded the Max-Planck junior research award as well as the research award of the Engelhorn foundation.
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"In summary, Gunter Meister has compiled a most timely textbook that gives an excellent overview of the fundamental biological role of RNA molecules. The book is a valuable resource of information for anyone interested in RNA biology. Its content goes well beyond the scope of standard molecular biology or
biochemistry textbooks." (ChemMedChem, 2011)

"Meister (biochemistry, U. of Regensburg, Germany) covers RNA biology comprehensively without getting into mechanistic detail, to provide an introduction for undergraduate students of all life sciences. Chapter-end references point to fuller treatments for students who are interested." (Book News, 1 October 2011)

 

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