RNA Biology

An Introduction

Häftad, Engelska, 2011

Av Gunter Meister, Germany) Meister, Gunter (University of Regensburg, Meister

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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.

Produktinformation

Utgivningsdatum2011-04-06
Mått172 x 241 x 18 mm
Vikt739 g
FormatHäftad
SpråkEngelska
Antal sidor380
FörlagWiley-VCH Verlag GmbH
ISBN9783527322787

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Biovetenskap inom Naturvetenskap och teknik

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.

Preface xvPart One mRNA Biology 11 Introduction 31.1 RNA Building Blocks 41.2 RNA Folding 61.3 The RNA World Hypothesis 101.4 Functions of RNA 111.5 Protein Classes that are Required for RNA Function 121.5.1 RNA Binding Proteins 121.5.1.1 Proteins that Interact with Single Stranded RNAs 121.5.1.2 Proteins that Interact with Double Stranded RNAs 141.5.2 RNA Helicases 14References 152 Transcription of Pre-mRNAs 172.1 Structure and Organization of Protein Coding Genes 182.2 Transcription of Mrnas by Rna Polymerase II 202.2.1 Transcriptional Initiation of Protein Coding Genes 232.2.2 Regulation of Transcriptional Initiation of Rna Polymerase II 272.2.3 Transition from Preinitiation to Initiation and Promoter Clearance 272.2.4 Productive Elongation of mRNA Transcripts 292.2.4.1 The Nucleotide Addition Cycle (NAC) 292.2.4.2 Protein Factors that Influence Pol II Elongation 302.3 Transcriptional Termination of Pre-mRNAs 312.4 Transcription is Coupled to Other mRNA Maturation Steps 322.5 Summary 34References 353 Capping of the Pre-mRNA 5 0 End 373.1 m 7 G-cap Structure 373.2 mRNA Capping Enzymes 393.2.1 RNA Triphosphatase 393.2.2 Guanylyltransferase 393.2.3 Guanine-N7-Methyltransferase 403.3 5 0 Capping is Coupled to Transcription 413.4 5 0 Cap Binding Proteins 413.5 Summary 42References 434 3 0 End Processing of Pre-mRNAs 454.1 Polyadenylation Signals 464.2 Proteins Involved in 3 0 End Processing of Pre-mRNAs 474.2.1 Cleavage and Polyadenylation Specific Factor (CPSF) 474.2.2 Cleavage Stimulation Factor (CstF) 474.2.3 Mammalian Cleavage Factor I (CFI m) and II (CFII m) 484.2.4 The Poly(A) Polymerase (PAP) 494.2.5 Poly(A)-Binding Protein (PABP) 504.2.6 Symplekin 514.3 3 0 End Processing is Tightly Linked to Transcriptional Termination 514.4 Alternative Polyadenylation 514.5 Cytoplasmic Polyadenylation 534.6 3 0 End Processing of Histone mRNAs 544.7 Summary 56References 575 Splicing of Eukaryotic Pre-mRNAs 595.1 Group I, II and III Introns 595.1.1 Group I Introns 595.1.2 Group II Introns 615.1.3 Group III Introns 615.2 The Mechanism of pre-mRNA Splicing 615.3 The Spliceosome 625.4 The U12-Dependent Minor Spliceosome 665.5 Coupling of Splicing with Transcription and 5 0 Capping 675.6 Alternative Splicing and the Complexity of Genomes 685.6.1 Mechanisms of Exon Inclusion into the Mature mRNA 695.6.2 Mechanism of Exon Exclusion from the Mature mRNA 705.7 Summary 705.8 Questions 71References 726 mRNA Export from the Nucleus to the Cytoplasm 736.1 Nuclear Import and Nuclear Export 736.2 mRNA Export Receptors 756.3 Adaptors that Bridge mRNAs with Export Receptors 786.4 Mechanism of mRNA Export 786.5 Coupling of mRNP Export to Other Steps of mRNA Maturation 806.6 Summary 806.7 Questions 81References 817 Translation 837.1 Amino Acids, mRNAs, tRNAs 837.1.1 mRNA 837.1.2 Amino Acids 847.1.3 Transfer RNAs (tRNAs) 867.1.4 Loading Amino Acids onto tRNAs 877.2 The Ribosome 897.3 The Mechanisms of Translation 907.3.1 Translation Initiation 907.3.1.1 Eukaryotes 907.3.1.2 Bacteria 937.3.1.3 Archaea 967.3.1.4 Internal Ribosome Entry Sites (IRESs) 967.3.2 Elongation 977.3.2.1 Polyribosomes 977.3.3 Termination 997.3.4 Recycling of the Ribosome 1007.4 Translational Regulation 1007.4.1 Regulation of Translation Initiation 1007.4.2 Regulation of Translation Elongation and Termination 1037.5 Coupling Translation with Other mRNA Maturation and Quality Control Steps 1037.6 Summary 1047.7 Questions 105References 1068 Deadenylation of mRNA 1078.1 Deadenylating Enzymes 1078.1.1 Poly(A) Nuclease 1078.1.2 CCR4-NOT Complex 1088.1.3 Poly(A) Ribonuclease 1088.1.4 Other Deadenylases 1108.2 Summary 1118.3 Questions 111References 1129 mRNA Decapping 1139.1 Decapping Enzymes are the Core of the mRNA Decapping Machinery 1139.2 Scavenger Decapping Enzyme DcpS 1159.3 Regulation of mRNA Decapping 1159.3.1 Inhibitors of Decapping 1159.3.2 Enhancers of Decapping 1169.4 Intracellular Localization of mRNA Decapping 1179.5 Summary 1189.6 Questions 119References 11910 mRNA Decay Pathways 12110.1 Deadenylation-Dependent mRNA Decay 12210.1.1 The 5 0 to 3 0 Exoribonuclease Xrn 1 12210.1.2 The Exosome 12210.1.2.1 Structural Organization of the Exosome 12510.1.2.2 Mechanism of Exosome-Mediated RNA Degradation 12510.1.2.3 Regulation of Exosome Activity 12610.2 Deadenylation-Independent mRNA Decay 12710.3 Endoribonuclease-Mediated mRNA Decay 12810.3.1 Eukaryotic Endoribonucleases 12910.4 Regulation of mRNA Decay 13110.5 RNA Degradation in Bacteria 13110.6 Summary 13310.7 Questions 134References 13511 mRNA Quality Control 13711.1 Nuclear mRNA Quality Control Mechanisms 13711.1.1 MRNP Retention at the Transcription Site 13811.1.2 MRNP Quality Control at the Nuclear Pore Complex 13811.2 Nonsense-Mediated mRNA Decay (NMD) 13811.2.1 Protein Factors Required for NMD 13911.2.1.1 UPF Proteins 13911.2.1.2 The Exon–Exon–Junction Complex (EJC) and Nmd 14011.2.1.3 SMG Proteins and the Phosphorylation of UPF 1 14111.2.2 Mechanism of NMD in Mammals 14211.2.3 Cytoplasmic Processing Bodies and NMD 14311.2.4 Mechanism of NMD in Yeast and Flies 14411.2.5 mRNA Degradation Pathways in NMD 14611.3 Other mRNA Quality Control Pathways 14611.3.1 Non-Stop mRNA Degradation 14611.3.2 No-Go mRNA Decay (NGD) 14811.4 Summary 14811.5 Questions 149References 149Part Two Non-Coding RNA Biology 15112 Ribosomal RNAs and the Biogenesis of Ribosomes 15312.1 Genomic Organization of Ribosomal RNA Genes 15312.1.1 Bacteria and Archaea 15312.1.2 Eukaryotes 15512.1.2.1 28S, 18S and 5.8S rRNAs 15512.1.2.2 5S rRNA 15612.2 Transcription of Ribosomal RNA Genes 15712.2.1 RNA Polymerase I 15712.2.1.1 Initiation of Pol I Transcription 15812.2.1.2 Promoter Clearance, Transcript Elongation and Termination of Pol I Transcription 16012.2.1.3 Regulation of RNA Polymerase I Transcription 16112.2.2 RNA Polymerase III and the Transcription of the 5S rRNA 16212.2.2.1 Pol III Promoters 16312.2.2.2 Transcription Initiation and Elongation of Rna Polymerase III 16512.2.2.3 Initiation of Type 3 Promoters 16712.2.2.4 Termination and Re-Initiation 16812.3 Maturation of rRNAs 16912.3.1 Small Nucleolar RNAs are Required for Pre-rRNA Processing 17012.4 Assembly of Ribosomal Subunits 17212.5 Nuclear Export of Ribosomal Subunits 17412.6 Modification, Structure and Function of rRNAs 17512.7 Summary 17812.8 Questions 179References 18013 Transfer RNAs 18313.1 Genomic Organization and Transcription of tRNA Genes 18313.2 Processing to Mature tRNAs 18413.2.1 5 0 Maturation of tRNAs by the RNase P Enzyme Complex 18413.2.2 3 0 End Maturation of tRNAs 18613.2.3 tRNA Splicing 18813.3 tRNA Modifications 19113.4 Nuclear Export of tRNAs 19313.5 Tertiary Structure of tRNAs 19413.6 Summary 196References 19714 The 7SL RNA and the Signal Recognition Particle 19914.1 Architecture of the SRP 19914.1.1 The SRP RNA 19914.1.2 Protein Components of the SRP 20114.1.2.1 Eukaryotes 20114.1.2.2 Archaea and Bacteria 20314.2 SRP-Mediated Protein Translocation 20414.3 Summary 206References 20815 Regulation of Transcription: the 7SK Small Nuclear RNA 20915.1 Architecture of the 7SK snRNA 20915.1.1 The 7SK snRNA 20915.1.2 Protein Components of the 7SK snRNP 21015.2 The 7SK snRNP Functions as Transcriptional Regulator 21215.2.1 P-TEFb Function in Transcription 21215.2.2 Repression of P-TEFb by the 7SK snRNP 21415.3 Other Small Non-Coding RNAs that Interfere with Transcription 21415.3.1 The 6S RNA in Bacteria 21415.3.2 Alu, B1 and B2 Non-Coding RNAs in Mammals 21515.4 Summary 215References 21616 Small Nucleolar RNAs 21716.1 Genomic Organization and snoRNA Transcription 21716.2 Box H/ACA snoRNAs 21816.3 Box C/D snoRNAs 22116.4 Maturation of Functional snoRNPs 22316.5 Orphan snoRNAs 22416.6 The Telomerase RNP 22616.7 Summary 227References 22817 Spliceosomal Small Nuclear RNAs 22917.1 Transcription and Maturation of Spliceosomal snRNAs 22917.1.1 Transcription of Spliceosomal snRNAs 22917.1.2 snRNA Maturation 23017.1.3 SnRNA Export to the Cytoplasm 23117.2 The Structure of UsnRNPs 23217.2.1 Secondary Structure of Spliceosomal snRNAs 23217.2.2 Protein Composition of UsnRNPs 23317.2.2.1 The Sm/LSm Core Structure 23317.2.2.2 UsnRNP-Specific Proteins 23517.3 Assembly of Spliceosomal snRNPs 23717.3.1 Cytoplasmic Assembly of the Sm Core Domain 23717.3.2 Formation of the Tri-Methyl Guanine Cap 24017.3.3 Import of Assembled UsnRNPs into the Nucleus 24117.4 Summary 24217.5 Questions 243References 24418 Small Non-Coding RNAs and the Mechanism of Gene Silencing 24518.1 Short Interfering RNAs and the Mechanism of RNA Interference 24518.2 Dicer 24818.3 RNA-Dependent RNA Polymerases 24818.4 Argonaute Proteins 25118.5 microRNAs and the Regulation of Gene Expression 25118.5.1 MiRNA Biogenesis 25118.5.2 Non-Canonical miRNA Biogenesis Pathways 25318.5.3 miRNA Functions 25518.5.3.1 miRNAs Can Act as siRNAs 25518.5.3.2 miRNAs Inhibit Translation 25518.5.3.3 miRNAs Induce Deadenylation and mRNA Decay 25618.6 PiRNAs and the Regulation of Mobile Genetic Elements in the Germ Line 25718.6.1 Transposons as Driving Force Behind Evolution 25818.6.2 PiRNAs Control Transposon Expression 25918.7 Small RNAs with Functions in Chromatin Regulation 26118.8 The CRISPR System – A Bacterial and Archaeal Defense Mechanism 26318.8.1 The CRISPR Locus 26318.8.2 Acquisition of CRISPR-Mediated Resistance 26418.8.3 Mechanism of CRISPR Activity 26518.9 Summary 266References 26919 Long Non-Coding RNAs 27119.1 The XIST Non-Coding RNA and X Chromosome Inactivation 27119.1.1 The X-Chromosome Inactivation Center (XIC) 27219.1.2 the Xist Non-coding Rna and the Mechanism of X Inactivation 27219.1.3 Regulation of XIST Function 27419.2 Dosage Compensation in Flies 27519.3 Non-Coding RNAs and the Regulation of Imprinting 27619.4 The Regulation of HOX Genes by Long Non-Coding RNAs 27819.5 Long non-Coding RNAs are Common in Complex Genomes 27819.6 Summary 278References 28020 RNA Editing 28120.1 RNA Editing by U Insertions or Deletions 28120.1.1 Mechanisms of U Insertions or Deletions 28220.2 RNA Editing by Base Modification 28320.2.1 c to U conversion 28420.2.2 Adenine to Inosine Editing 28620.2.2.1 Adenosine Deaminase Acting on RNA 28720.2.2.2 Editing Site Selectivity 28820.2.2.3 Biological Consequences of A to I Conversions 28820.3 Summary 290References 29121 Ribozymes – Catalytic RNA Molecules 29321.1 Identification of Catalytic RNAs 29321.2 Mechanisms and Secondary Structures of Different Ribozymes 29421.2.1 Group I Introns 29421.2.2 RNase P 29521.2.3 The Diels–Alderase Ribozyme 29621.2.4 Hammerhead Ribozymes 29821.2.5 The glmS Ribozyme 29821.3 Summary 300References 30122 Riboswitches and RNA Sensors 30322.1 Mechanisms of Riboswitch Function 30322.2 Riboswitch Structures 30522.3 RNA Thermometers 30522.4 Summary 307References 30823 RNomics 30923.1 ‘‘Omics’’ Approaches 30923.2 Experimental RNA Profiling Strategies 31023.2.1 Northern Blotting 31023.2.2 Microarray 31123.2.3 Quantitative PCR 31323.2.4 RNA Fluorescent In Situ Hybridization 31423.2.5 Next Generation Sequencing 31423.3 RNA Biology and the Complexity of Genomes 31523.4 Summary 315References 318Appendix: Answers to Questions 319Index 355

"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 orbiochemistry 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)