Meister G. RNA biology: an introduction (Weinheim, 2011). - ОГЛАВЛЕНИЕ / CONTENTS
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ОбложкаMeister G. RNA biology: an introduction. - Weinheim: Wiley-VCH, 2011. - xvi, 363 p.: ill. (some col.). - Incl. bibl. ref. - Ind.: p.355-363. - ISBN 978-3-527-32278-7
 

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Оглавление / Contents
 
   Preface ..................................................... XV

Part One  mRNA Biology .......................................... 1
1  Introduction ................................................. 3
   1.1  RNA Building Blocks ..................................... 4
   1.2  RNA Folding ............................................. 6
   1.3  The RNA World Hypothesis ............................... 10
   1.4  Functions of RNA ....................................... 11
   1.5  Protein Classes that are Required for RNA Function ..... 12
        1.5.1  RNA Binding Proteins ............................ 12
        1.5.2  RNA Helicases ................................... 14
   References .................................................. 15
2  Transcription of Pre-mRNAs .................................. 17
   2.1  Structure and Organization of Protein Coding Genes ..... 18
   2.2  Transcription of mRNAs by RNA Polymerase II ............ 20
        2.2.1  Transcriptional Initiation of Protein Coding
               Genes ........................................... 23
        2.2.2  Regulation of Transcriptional Initiation of
               RNA Polymerase II ............................... 27
        2.2.3  Transition from Preinitiation to Initiation
               and Promoter Clearance
        2.2.4  Productive Elongation of mRNA Transcripts ....... 29
   2.3  Transcriptional Termination of Pre-mRNAs ............... 31
   2.4  Transcription is Coupled to Other mRNA Maturation
        Steps .................................................. 32
   2.5  Summary ................................................ 34
   References .................................................. 35
3  Capping of the Pre-mRNA 5' End .............................. 37
   3.1  m7G-cap Structure ...................................... 37
   3.2  mRNA Capping Enzymes ................................... 39
        3.2.1  RNA Triphosphatase .............................. 39
        3.2.2  Guanylyltransferase ............................. 39
        3.2.3  Guanine-N7-Methyltransferase .................... 40
   3.3  5' Capping is Coupled to Transcription ................. 41
   3.4  5' Cap Binding Proteins ................................ 41
   3.5  Summary ................................................ 42
   References .................................................. 43
4  3' End Processing of Pre-mRNAs .............................. 45
   4.1  Polyadenylation Signals ................................ 46
   4.2  Proteins Involved in 3' End Processing of Pre-mRNAs .... 47
        4.2.1  Cleavage and Polyadenylation Specific Factor
               (CPSF) .......................................... 47
        4.2.2  Cleavage Stimulation Factor (CstF) .............. 47
        4.2.3  Mammalian Cleavage Factor I (CFIm) and II
               (CFIIm) ......................................... 48
        4.2.4  The Poly(A) Polymerase (PAP) .................... 49
        4.2.5  Poly(A)-Binding Protein (PABP) .................. 50
        4.2.6  Symplekin ....................................... 51
   4.3  3' End Processing is Tightly Linked to
        Transcriptional Termination ............................ 51
   4.4  Alternative Polyadenylation ............................ 51
   4.5  Cytoplasmic Polyadenylation ............................ 53
   4.6  3' End Processing of Histone mRNAs ..................... 54
   4.7  Summary ................................................ 56
   References .................................................. 57
5  Splicing of Eukaryotic Pre-mRNAs ............................ 59
   5.1  Group I, II and III Introns ............................ 59
        5.1.1  Group I Introns ................................. 59
        5.1.2  Group II Introns ................................ 61
        5.1.3  Group III Introns ............................... 61
   5.2  The Mechanism of pre-mRNA Splicing ..................... 61
   5.3  The Spliceosome ........................................ 62
   5.4  The U12-Dependent Minor Spliceosome .................... 66
   5.5  Coupling of Splicing with Transcription and 5'
        Capping ................................................ 67
   5.6  Alternative Splicing and the Complexity of Genomes ..... 68
        5.6.1  Mechanisms of Exon Inclusion into the Mature
               mRNA ............................................ 69
        5.6.2  Mechanism of Exon Exclusion from the Mature
               mRNA ............................................ 70
   5.7  Summary ................................................ 70
   5.8  Questions .............................................. 71
   References .................................................. 72
6  mRNA Export from the Nucleus to the Cytoplasm ............... 73
   6.1  Nuclear Import and Nuclear Export ...................... 73
   6.2  mRNA Export Receptors .................................. 75
   6.3  Adaptors that Bridge mRNAs with Export Receptors ....... 78
   6.4  Mechanism of mRNA Export ............................... 78
   6.5  Coupling of mRNP Export to Other Steps of mRNA
        Maturation ............................................. 80
   6.6  Summary ................................................ 80
   6.7  Questions .............................................. 81
   References .................................................. 81
7  Translation ................................................. 83
   7.1  Amino Acids, mRNAs, tRNAs .............................. 83
        7.1.1  mRNA ............................................ 83
        7.1.2  Amino Acids ..................................... 84
        7.1.3  Transfer RNAs (tRNAs) ........................... 86
        7.1.4  Loading Amino Acids onto tRNAs .................. 87
   7.2  The Ribosome ........................................... 89
        7.3.1  Translation Initiation .......................... 90
        7.3.2  Elongation ...................................... 97
        7.3.3  Termination ..................................... 99
        7.3.4  Recycling of the Ribosome ...................... 100
   7.4  Translational Regulation .............................. 100
        7.4.1  Regulation of Translation Initiation ........... 100
        7.4.2  Regulation of Translation Elongation and
               Termination .................................... 103
   7.5  Coupling Translation with Other mRNA Maturation and
        Quality Control Steps ................................. 103
   7.6  Summary ............................................... 104
   7.7  Questions ............................................. 105
   References ................................................. 106
8  Deadenylation of mRNA ...................................... 107
   8.1  Deadenylating Enzymes ................................. 107
        8.1.1  Poly(A) Nuclease ............................... 107
        8.1.2  CCR4-NOT Complex ............................... 108
        8.1.3  Poly(A) Ribonuclease ........................... 108
        8.1.4  Other Deadenylases ............................. 110
   8.2  Summary ............................................... 111
   8.3  Questions ............................................. 111
   References ................................................. 112
9  mRNA Decapping ............................................. 113
   9.1  Decapping Enzymes are the Core of the mRNA Decapping
        Machinery ............................................. 113
   9.2  Scavenger Decapping Enzyme DcpS ....................... 115
   9.3  Regulation of mRNA Decapping .......................... 115
        9.3.1  Inhibitors of Decapping ........................ 115
        9.3.2  Enhancers of Decapping ......................... 116
   9.4  Intracellular Localization of mRNA Decapping .......... 117
   9.5  Summary ............................................... 118
   9.6  Questions ............................................. 119
   References ................................................. 119
10 mRNA Decay Pathways ........................................ 121
   10.1 Deadenylation-Dependent mRNA Decay .................... 122
        10.1.1 The 5' to 3' Exoribonuclease Xrnl .............. 122
        10.1.2 The Exosome .................................... 122
   10.2 Deadenylation-Independent mRNA Decay .................. 127
   10.3 Endoribonuclease-Mediated mRNA Decay .................. 128
   10.3.1 Eukaryotic Endoribonucleases ........................ 129
   10.4 Regulation of mRNA Decay .............................. 131
   10.5 RNA Degradation in Bacteria ........................... 131
   10.6 Summary ............................................... 133
   10.7 Questions ............................................. 134
   References ................................................. 135
11 mRNA Quality Control ....................................... 137
   11.1 Nuclear mRNA Quality Control Mechanisms ............... 137
        11.1.1 MRNP Retention at the Transcription Site ....... 138
        11.1.2 MRNP Quality Control at the Nuclear Pore
               Complex ........................................ 138
   11.2 Nonsense-Mediated mRNA Decay (NMD) .................... 138
        11.2.1 Protein Factors Required for NMD ............... 139
        11.2.2 Mechanism of NMD in Mammals .................... 142
        11.2.3 Cytoplasmic Processing Bodies and NMD .......... 143
        11.2.4 Mechanism of NMD in Yeast and Flies ............ 144
        11.2.5 mRNA Degradation Pathways in NMD ............... 146
   11.3 Other mRNA Quality Control Pathways ................... 146
        11.3.1 Non-Stop mRNA Degradation ...................... 146
        11.3.2 No-Go mRNA Decay (NGD) ......................... 148
   11.4 Summary ............................................... 148
   11.5 Questions ............................................. 149
   References ................................................. 149

Part Two Non-Coding RNA Biology ............................... 151

12 Ribosomal RNAs and the Biogenesis of Ribosomes ............. 153
   12.1 Genomic Organization of Ribosomal RNA Genes ........... 153
        12.1.1 Bacteria and Archaea ........................... 153
        12.1.2 Eukaryotes ..................................... 155
   12.2 Transcription of Ribosomal RNA Genes .................. 157
        12.2.1 RNA Polymerase I ............................... 157
        12.2.2 RNA Polymerase III and the Transcription of
               the 5S rRNA .................................... 162
   12.3 Maturation of rRNAs ................................... 169
        12.3.1 Small Nucleolar RNAs are Required for
               Pre-rRNA Processing ............................ 170
   12.4 Assembly of Ribosomal Subunits ........................ 172
   12.5 Nuclear Export of Ribosomal Subunits .................. 174
   12.6 Modification, Structure and Function of rRNAs ......... 175
   12.7 Summary ............................................... 178
   12.8 Questions ............................................. 179
   References ................................................. 180
13 Transfer RNAs .............................................. 183
   13.1 Genomic Organization and Transcription of tRNA
        Genes ................................................. 183
   13.2 Processing to Mature tRNAs ............................ 184
        13.2.1 5' Maturation of tRNAs by the RNase P Enzyme
               Complex ........................................ 184
        13.2.2 3' End Maturation of tRNAs ..................... 186
        13.2.3 tRNA Splicing .................................. 188
   13.3 tRNA Modifications .................................... 191
   13.4 Nuclear Export of tRNAs ............................... 193
   13.5 Tertiary Structure of tRNAs ........................... 194
   13.6 Summary ............................................... 196
   References ................................................. 197
14 The 7SL RNA and the Signal Recognition Particle ............ 199
   14.1 Architecture of the SRP ............................... 199
        14.1.1 The SRP RNA .................................... 199
        14.1.2 Protein Components of the SRP .................. 201
   14.2 SRP-Mediated Protein Translocation .................... 204
   14.3 Summary ............................................... 206
   References ................................................. 208
15 Regulation of Transcription: the 7SK Small Nuclear RNA ..... 209
   15.1 Architecture of the 7SK snRNA ......................... 209
        15.1.1 The 7SK snRNA .................................. 209
        15.1.2 Protein Components of the 7SK snRNP ............ 210
   15.2 The 7SK snRNP Functions as Transcriptional
        Regulator ............................................. 212
        15.2.1 P-TEFb Function in Transcription ............... 212
        15.2.2 Repression of P-TEFb by the 7SK snRNP .......... 214
   15.3 Other Small Non-Coding RNAs that Interfere with
        Transcription ......................................... 214
        15.3.1 The 6S RNA in Bacteria ......................... 214
        15.3.2 Alu, B1 and B2 Non-Coding RNAs in Mammals ...... 215
   15.4 Summary ............................................... 215
   References ................................................. 216
16 Small Nucleolar RNAs ....................................... 217
   16.1 Genomic Organization and snoRNA Transcription ......... 217
   16.2 Box H/ACA snoRNAs ..................................... 218
   16.3 Box C/D snoRNAs ....................................... 221
   16.4 Maturation of Functional snoRNPs ...................... 223
   16.5 Orphan snoRNAs ........................................ 224
   16.6 The Telomerase RNP .................................... 226
   16.7 Summary ............................................... 227
   References ................................................. 228
17 Spliceosomal Small Nuclear RNAs ............................ 229
   17.1 Transcription and Maturation of Spliceosomal snRNAs
        17.1.1 Transcription of Spliceosomal snRNAs ........... 229
        17.1.2 snRNA Maturation ............................... 230
        17.1.3 SnRNA Export to the Cytoplasm .................. 231
   17.2 The Structure of UsnRNPs .............................. 232
        17.2.1 Secondary Structure of Spliceosomal snRNAs ..... 232
        17.2.2 Protein Composition of UsnRNPs ................. 233
   17.3 Assembly of Spliceosomal snRNPs ....................... 237
        17.3.1 Cytoplasmic Assembly of the Sm Core Domain ..... 237
        17.3.2 Formation of the Tri-Methyl Guanine Cap ........ 240
        17.3.3 Import of Assembled UsnRNPs into the Nucleus ... 241
   17.4 Summary ............................................... 242
   17.5 Questions ............................................. 243
   References ................................................. 244
18 Small Non-Coding RNAs and the Mechanism of Gene
   Silencing .................................................. 245
   18.1 Short Interfering RNAs and the Mechanism of RNA
        Interference .......................................... 245
   18.2 Dicer ................................................. 248
   18.3 RNA-Dependent RNA Polymerases ......................... 248
   18.4 Argonaute Proteins .................................... 251
   18.5 microRNAs and the Regulation of Gene Expression ....... 251
        18.5.1 MiRNA Biogenesis ............................... 251
        18.5.2 Non-Canonical miRNA Biogenesis Pathways ........ 253
        18.5.3 miRNA Functions ................................ 255
   18.6 PiRNAs and the Regulation of Mobile Genetic Elements
        in the Germ Line ...................................... 257
        18.6.1 Transposons as Driving Force Behind
               Evolution ...................................... 258
        18.6.2 PiRNAs Control Transposon Expression ........... 259
   18.7 Small RNAs with Functions in Chromatin Regulation ..... 261
   18.8 The CRISPR System - A Bacterial and Archaeal Defense
        Mechanism ............................................. 263
        18.8.1 The CRISPR Locus ............................... 263
        18.8.2 Acquisition of CRISPR-Mediated Resistance ...... 264
        18.8.3 Mechanism of CRISPR Activity ................... 265
   18.9 Summary ............................................... 266
   References ................................................. 269
19 Long Non-Coding RNAs ....................................... 271
   19.1 The XIST Non-Coding RNA and X Chromosome
        Inactivation .......................................... 271
        19.1.1 The X-Chromosome Inactivation Center (XIC) ..... 272
        19.1.2 The XIST Non-Coding RNA and the Mechanism of
               X Inactivation ................................. 272
        19.1.3 Regulation of XIST Function .................... 274
   19.2 Dosage Compensation in Flies .......................... 275
   19.3 Non-Coding RNAs and the Regulation of Imprinting ...... 276
   19.4 The Regulation of HOX Genes by Long Non-Coding RNAs ... 278
   19.5 Long non-Coding RNAs are Common in Complex Genomes .... 278
   19.6 Summary ............................................... 278
   References ................................................. 280
20 RNA Editing ................................................ 281
   20.1 RNA Editing by U Insertions or Deletions .............. 281
        20.1.1 Mechanisms of U Insertions or Deletions ........ 282
   20.2 RNA Editing by Base Modification ...................... 283
        20.2.1 С to U Conversion .............................. 284
        20.2.2 Adenine to Inosine Editing ..................... 286
   20.3 Summary ............................................... 290
   References ................................................. 291
21 Ribozymes - Catalytic RNA Molecules ........................ 293
   21.1 Identification of Catalytic RNAs ...................... 293
   21.2 Mechanisms and Secondary Structures of Different
        Ribozymes ............................................. 294
        21.2.1 Group I Introns ................................ 294
        21.2.2 RNase P ........................................ 295
        21.2.3 The Diels-Alderase Ribozyme .................... 296
        21.2.4 Hammerhead Ribozymes ........................... 298
        21.2.5 The glmS Ribozyme .............................. 298
   21.3 Summary ............................................... 300
   References ................................................. 301
22 Riboswitches and RNA Sensors ............................... 303
   22.1 Mechanisms of Riboswitch Function ..................... 303
   22.2 Riboswitch Structures ................................. 305
   22.3 RNA Thermometers ...................................... 305
   22.4 Summary ............................................... 307
   References ................................................. 308
23 RNomics .................................................... 309
   23.1 "Omics" Approaches .................................... 309
   23.2 Experimental RNA Profiling Strategies ................. 310
        23.2.1 Northern Blotting .............................. 310
        23.2.2 Microarray ..................................... 311
        23.2.3 Quantitative PCR ............................... 313
        23.2.4 RNA Fluorescent In Situ Hybridization .......... 314
        23.2.5 Next Generation Sequencing ..................... 314
   23.3 RNA Biology and the Complexity of Genomes ............. 315
   23.4 Summary ............................................... 315
   References ................................................. 318

   Appendix: Answers to Questions ............................. 319
   Index ...................................................... 355


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