Latchman Eukaryotic Transcription Factors

5. Auflage 2010
ISBN: 978-0-08-056103-5
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 488 Seiten

Transcription, or the process by which DNA produces RNA, is a central aspect of gene expression. Transcription factors regulate transcription during development and in disease states. As such, it is critical for researchers to gain a good understanding of the relationship between the structure of various families of transcription factors and their function, as well as roles in human disease. Since publication of the Fourth Edition, there have been major advances, notably in the areas of chromatin remodeling and genome-scale analyses. This complete update includes all new coverage of the latest developments, from enabling genomic technologies to studies on the importance of post-translational modifications beyond phosphorylation events.
Brand new coverage in this edition includes:
* Potential of transcription factors as therapeutic targets in human disease
* Importance of histone modifications
* Use of genome-based sequence analysis and high-throughput methods
* Applications of the chromatin immunoprecipitation (ChIP) assay
* Transcriptional elongation
* Regulation by post-translational modifications
* Regulatory networks and bioinformatics

Autoren/Hrsg.

Latchman, David S.

Inhaltsverzeichnis

1;Front cover;1
2;Eukaryotic transcription factors;4
3;Copyright page;5
4;Contents;8
5;List of tables;14
6;About the author;16
7;Preface;18
8;Preface to the fourth edition;20
9;Preface to the third edition;22
10;Preface to the second edition;24
11;Preface to the first edition;26
12;Acknowledgements;28
13;CHAPTER 1. DNA SEQUENCES, TRANSCRIPTION FACTORS AND CHROMATIN STRUCTURE;30
13.1;1.1. The importance of transcription;30
13.2;1.2. Chromatin structure and its remodelling;31
13.2.1;1.2.1. Chromatin structure and gene regulation;31
13.2.2;1.2.2. Chromatin remodelling factors;33
13.2.3;1.2.3. Histone modifications;34
13.3;1.3. DNA sequence elements;38
13.3.1;1.3.1. The gene promoter;38
13.3.2;1.3.2. Sequences involved in the basic process of transcription;39
13.3.3;1.3.3. Sequences involved in regulated transcription;40
13.3.4;1.3.4. Sequences which act at a distance;44
13.3.5;1.3.5. Negatively acting DNA sequences;49
13.3.6;1.3.6. Interaction between factors bound at various sites;50
13.4;1.4. Conclusions;52
13.5;References;53
14;CHAPTER 2. METHODS FOR STUDYING TRANSCRIPTION FACTORS;58
14.1;2.1. Introduction;58
14.2;2.2. Methods for studying DNA–protein interactions;58
14.2.1;2.2.1. DNA mobility shift assay;58
14.2.2;2.2.2. DNAseI footprinting assay;62
14.2.3;2.2.3. Methylation interference assay;66
14.2.4;2.2.4. In vivo footprinting assay;67
14.3;2.3. Methods for purifying and/or cloning transcription factors;71
14.3.1;2.3.1. Protein purification;71
14.3.2;2.3.2. Gene cloning;75
14.4;2.4. Use of cloned genes;80
14.4.1;2.4.1. Domain mapping of transcription factors;80
14.4.2;2.4.2. Determining the DNA binding specificity of an uncharacterized factor;84
14.4.3;2.4.3. Identification of target genes for transcription factors;86
14.5;2.5. Conclusions;91
14.6;References;92
15;CHAPTER 3. RNA POLYMERASES AND THE BASAL TRANSCRIPTIONAL COMPLEX;97
15.1;3.1. RNA polymerases;97
15.2;3.2. The stable transcriptional complex;99
15.3;3.3. RNA polymerase I;100
15.4;3.4. RNA polymerase III;102
15.5;3.5. RNA polymerase II;105
15.5.1;3.5.1. Stepwise assembly of the RNA polymerase II basal transcriptional complex;105
15.5.2;3.5.2. The RNA polymerase holoenzyme;109
15.6;3.6. TBP: the universal transcription factor?;110
15.7;3.7. Transcriptional elongation;117
15.8;3.8. Conclusions;119
15.9;References;119
16;CHAPTER 4. FAMILIES OF DNA BINDING TRANSCRIPTION FACTORS;125
16.1;4.1. Introduction;125
16.2;4.2. The homeodomain;126
16.2.1;4.2.1. Transcription factors in Drosophila development;126
16.2.2;4.2.2. The homeobox;127
16.2.3;4.2.3. DNA binding by the helix-turn-helix motif in the homeobox;129
16.2.4;4.2.4. Regulation of DNA binding specificity by interactions between different homeobox proteins;137
16.2.5;4.2.5. Homeodomain transcription factors in other organisms;141
16.2.6;4.2.6. POU proteins;143
16.2.7;4.2.7. Pax proteins;153
16.3;4.3. The two cysteine two histidine Zinc finger;155
16.3.1;4.3.1. Transcription factors with the two cysteine two histidine finger;155
16.3.2;4.3.2. DNA binding by the two cysteine two histidine finger;157
16.4;4.4. The multi-cysteine Zinc finger;160
16.4.1;4.4.1. Nuclear receptors;160
16.4.2;4.4.2. DNA binding by the multi-cysteine zinc finger;162
16.5;4.5. The basic DNA binding domain;171
16.5.1;4.5.1. The leucine zipper and the basic DNA binding domain;171
16.5.2;4.5.2. The helix-loop-helix motif and the basic DNA binding domain;176
16.5.3;4.5.3. Dimerization of basic DNA binding domain-containing factors;178
16.6;4.6. Other DNA binding motifs;180
16.7;4.7. Conclusions;181
16.8;References;183
17;CHAPTER 5. ACTIVATION OF GENE EXPRESSION BY TRANSCRIPTION FACTORS;190
17.1;5.1. Activation domains;190
17.2;5.2. Nature of activation domains;192
17.2.1;5.2.1. Acidic domains;192
17.2.2;5.2.2. Glutamine-rich domains;195
17.2.3;5.2.3. Proline-rich domains;195
17.2.4;5.2.4. Functional relationship of the different activation domains;196
17.3;5.3. Interaction of activation domains with the basal transcriptional complex;197
17.3.1;5.3.1. Activators and the basal transcriptional complex;197
17.3.2;5.3.2. Stimulation of factor binding;199
17.3.3;5.3.3. Stimulation of factor activity;202
17.4;5.4. Interaction of activation domains with other regulatory proteins;206
17.4.1;5.4.1. The mediator complex;206
17.4.2;5.4.2. TAFs;209
17.4.3;5.4.3. CBP and other co-activators;216
17.4.4;5.4.4. A multitude of targets for transcriptional activators;222
17.5;5.5. Effect of transcriptional activators on chromatin structure;224
17.5.1;5.5.1. Effect of chromatin remodelling factors;224
17.5.2;5.5.2. Effect on histone modification;232
17.5.3;5.5.3. Transcriptional activation by chromatin structure changes and by stimulation of the basal transcriptional complex;236
17.6;5.6. Stimulation of transcriptional elongation;241
17.7;5.7. Conclusions;246
17.8;References;250
18;CHAPTER 6. REPRESSION OF GENE EXPRESSION BY TRANSCRIPTION FACTORS;258
18.1;6.1. Repression of transcription;258
18.2;6.2. Indirect repression;259
18.2.1;6.2.1. Inhibition of activator binding by masking of its DNA binding site;259
18.2.2;6.2.2. Inhibition of activator binding by formation of a non-DNA binding complex;264
18.2.3;6.2.3. Quenching of an activator;266
18.2.4;6.2.4. Degradation of an activator;267
18.3;6.3. Direct repression;268
18.3.1;6.3.1. Mechanisms of transcriptional repression;268
18.3.2;6.3.2. Direct repression by DNA binding transcription factors;269
18.3.3;6.3.3. Direct repression by factors binding to the basal transcriptional complex;283
18.4;6.4. Inhibition by alteration of chromatin structure;287
18.4.1;6.4.1. Effect of repressors on chromatin;287
18.4.2;6.4.2. Small RNAs and transcriptional inhibition;293
18.5;6.5. Inhibition of transcriptional elongation;295
18.6;6.6. Conclusions;299
18.7;References;301
19;CHAPTER 7. REGULATION OF TRANSCRIPTION FACTOR SYNTHESIS;307
19.1;7.1. Transcription factor regulation;307
19.2;7.2. Regulated synthesis of transcription factors;307
19.2.1;7.2.1. The MyoD transcription factor;308
19.2.2;7.2.2. Homeobox transcription factors;317
19.3;7.3. Mechanisms regulating the synthesis of transcription factors;330
19.3.1;7.3.1. Regulation of transcription;330
19.3.2;7.3.2. Regulation of RNA splicing;333
19.3.3;7.3.3. Regulation of translation;340
19.4;7.4. Conclusions;343
19.5;References;344
20;CHAPTER 8. REGULATION OF TRANSCRIPTION FACTOR ACTIVITY;348
20.1;8.1. Evidence for the regulated activity of transcription factors;348
20.2;8.2. Regulation by protein–ligand binding;350
20.2.1;8.2.1. Examples of regulation by ligand binding;350
20.2.2;8.2.2. The nuclear receptors;353
20.3;8.3. Regulation by protein–protein interactions;361
20.3.1;8.3.1. Inhibition of transcription factor activity by protein–protein interaction;361
20.3.2;8.3.2. Activation of transcription factors by protein–protein interaction;371
20.3.3;8.3.3. Alteration of transcription factor function by protein–protein interaction;371
20.4;8.4. Regulation by protein modification;373
20.4.1;8.4.1. Transcription factor modification;373
20.4.2;8.4.2. Phosphorylation;373
20.4.3;8.4.3. Acetylation;383
20.4.4;8.4.4. Methylation;384
20.4.5;8.4.5. Ubiquitination and sumoylation;386
20.5;8.5. Regulation by protein degradation and processing;394
20.6;8.6. Role of regulated activity;398
20.7;8.7. Conclusions;400
20.8;References;402
21;CHAPTER 9. TRANSCRIPTION FACTORS AND HUMAN DISEASE;409
21.1;9.1. Diseases caused by transcription factor mutations;409
21.2;9.2. Cancer;416
21.3;9.3. Cellular oncogenes and cancer;418
21.3.1;9.3.1. Fos, Jun and AP1;418
21.3.2;9.3.2. v-erbA and the thyroid hormone receptor;424
21.3.3;9.3.3. The myc oncogene;428
21.3.4;9.3.4. Other oncogenic transcription factors;435
21.4;9.4 Anti-oncogenes and cancer;439
21.4.1;9.4.1. Nature of anti-oncogenes;439
21.4.2;9.4.2. p53;440
21.4.3;9.4.3. The Retinoblastoma protein;449
21.4.4;9.4.4. Other anti-oncogenic transcription factors;456
21.5;9.5. Transcription factors and treatment of human disease;461
21.6;9.6. Conclusions;471
21.7;References;473
22;CHAPTER 10. CONCLUSIONS AND FUTURE PROSPECTS;485
23;Index;489
23.1;A;489
23.2;B;490
23.3;C;490
23.4;D;492
23.5;E;493
23.6;F;494
23.7;G;495
23.8;H;495
23.9;I;497
23.10;J;498
23.11;K;498
23.12;L;498
23.13;M;499
23.14;N;500
23.15;O;501
23.16;P;501
23.17;Q;503
23.18;R;503
23.19;S;504
23.20;T;505
23.21;U;506
23.22;V;507
23.23;W;507
23.24;X;507
23.25;Y;507
23.26;Z;507
24;Color plates;274