Genome Transcriptome and Proteome Analysis

Genome, Transcriptome and Proteome Analysis......Page 3
Contents......Page 7
Preface......Page 13
About the Author......Page 15
Acknowledgements......Page 17
1.1.1 Nucleic acids......Page 19
1.1.2 Constituents of the genome......Page 21
1.1.3 Organelle genomes......Page 22
1.1.4 The structure of genes......Page 23
1.1.5 Transcription and translation......Page 24
1.1.6 Genes, multigene families and conserved sequences......Page 26
1.2.1 Restriction enzymes and electrophoresis......Page 27
1.2.3 Hybridization techniques......Page 29
1.2.4 Enzymatic amplification (PCR)......Page 32
1.2.6 Chromosomal assignment......Page 34
1.2.7 Techniques specific to genomic analysis......Page 36
1.3.1 Creation of the genome programmes......Page 38
1.3.3 The growing importance of bioinformatics......Page 40
1.4.1 The main branches of life......Page 43
1.4.2 Prokaryotes......Page 44
1.4.3 Eukaryotes......Page 46
2.1.1 The genetic maps of Drosophila and humans......Page 51
2.1.2 Tools for genetic mapping in humans......Page 53
2.1.3 RFLP markers......Page 54
2.1.5 Mapping methodology......Page 56
2.2.2 Microsatellites and modern maps......Page 58
2.2.4 SNP maps......Page 61
2.2.5 Genetic maps of model and domestic species......Page 64
2.2.6 Size of genetic maps......Page 66
2.3.2 The establishment of radiation hybrid maps......Page 68
2.3.4 Size of maps......Page 69
2.4 Conclusion......Page 70
3 Physical Maps......Page 71
3.1.2 Physical mapping of model species......Page 72
3.1.3 Local maps in humans......Page 75
3.2.2 The whole-genome approach......Page 76
3.2.3 STS mapping......Page 77
3.2.5 Mapping by hybridization......Page 79
3.3.1 The CEPH/Généthon map......Page 81
3.3.2 The WI/MIT map......Page 82
3.3.4 New generation human physical maps......Page 84
3.4 Conclusion......Page 87
4.1.1 Approaches used for large-scale sequencing......Page 89
4.1.2 Sequencing strategies......Page 90
4.1.3 Organisms sequenced......Page 93
4.1.4 Identifying genes......Page 96
4.2.1 Chromosome structure......Page 98
4.2.2 Gene organization......Page 99
4.2.3 Remarkable genes......Page 102
4.2.4 Virulence......Page 103
4.2.5 Non-coding sequences......Page 105
4.2.6 Comparative genomics......Page 108
4.3.1 Chromosome structure......Page 110
4.3.2 Identification of genes......Page 112
4.3.3 Functions of recognized or predicted genes......Page 113
4.3.4 Genes specific to metazoans......Page 116
4.3.5 Plant genomics......Page 117
4.3.6 Homologues of genes responsible for human disease......Page 119
4.3.7 Non-coding regions......Page 120
4.3.8 Evolutionary genomics......Page 121
4.4.1 Human chromosomes......Page 122
4.4.2 Identification of genes......Page 124
4.4.3 Repeated sequences......Page 128
4.4.4 Evolution......Page 129
4.5.1 Plasmodium falciparum......Page 131
4.5.2 Anopheles......Page 134
4.5.3 Microsporidium......Page 136
4.5.4 Leishmania major......Page 138
4.6 Conclusion......Page 139
5.1.1 Posing the problem......Page 141
5.1.2 Production and sequencing of cDNA......Page 142
5.1.3 Choice of tissue of origin......Page 143
5.1.4 Large-scale sequencing of cDNA......Page 144
5.2.2 The involvement of large pharmaceutical companies......Page 145
5.2.3 The ‘coining’ of partial sequences......Page 146
5.3.1 Assembly of partial sequences......Page 147
5.3.2 Identification of new genes......Page 148
5.3.4 Identification of genes responsible for genetic diseases......Page 149
5.3.5 cDNA programmes in animal and plant species......Page 150
5.4.2 Massive sequencing and the global vision of cellular physiology......Page 151
5.4.3 Use of nucleic acid chips......Page 154
5.4.4 The SAGE technique......Page 158
5.5 Conclusion......Page 163
6 The Proteome......Page 165
6.1.1 Electrophoresis......Page 166
6.1.3 Ultracentrifugation......Page 168
6.1.4 Use of antibodies......Page 170
6.1.5 Study of protein interactions......Page 172
6.1.6 Informatics......Page 173
6.2 Transgenesis......Page 174
6.2.1 Mouse transgenics......Page 175
6.2.2 Examples of mouse transgenics......Page 177
6.2.3 Transgenesis in other species......Page 178
6.3 Mutagenesis......Page 180
6.3.1 Directed mutagenesis......Page 181
6.3.2 Directed mutagenesis in mice (knock-out)......Page 183
6.3.3 Examples of knock-out in mice......Page 185
6.3.4 Random mutagenesis......Page 186
6.4 Two-dimensional Electrophoresis and Identification of Proteins......Page 187
6.4.1 Separation of proteins by two-dimensional electrophoresis......Page 188
6.4.2 Protein identification by classic techniques......Page 189
6.4.3 Identification of proteins by mass spectrometry......Page 191
6.4.4 Examples of applications......Page 195
6.4.5 Protein interactions......Page 196
6.5.1 Strategy......Page 197
6.5.2 Protein–protein interactions......Page 201
6.5.3 RNA–protein interactions......Page 203
6.5.4 Global approaches......Page 204
6.6.1 Construction of protein chips......Page 206
6.6.2 Strategies employed......Page 207
6.7.1 Crystallography......Page 209
6.7.3 Protein structure......Page 210
6.7.4 Example: histocompatibility antigens......Page 211
6.8 Conclusion......Page 212
7.1.1 Monogenic and multifactorial diseases......Page 215
7.1.2 Mutations......Page 217
7.1.3 Cloning genes responsible for diseases......Page 219
7.2.1 Examples of functional cloning......Page 220
7.2.2 Chromosomal anomalies......Page 222
7.3.2 Genetic mapping and primary localization......Page 223
7.3.4 Identification of genes present in a localization interval, and of the disease-causing gene......Page 225
7.3.5 The first success of positional cloning......Page 226
7.4.1 Monogenic diseases......Page 227
7.4.2 Multifactorial diseases......Page 229
7.4.4 Towards a redefinition of some genetic diseases......Page 230
7.4.5 New mutational mechanisms......Page 231
7.4.6 Genetic diseases and therapies......Page 233
7.5 Conclusion......Page 236
General Conclusion......Page 237
Further Reading......Page 239
Index......Page 241