Elsevier S & T

Eukaryotic Transcription Factors

Latchman, David; Latchman, David S.

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Table of contents
  • Contentsvii
  • List of tablesxiii
  • About the authorxv
  • Prefacexvii
  • Preface to the fourth editionxix
  • Preface to the third editionxxi
  • Preface to the second editionxxiii
  • Preface to the first editionxxv
  • Acknowledgementsxxvii
  • CHAPTER 1. DNA SEQUENCES, TRANSCRIPTION FACTORS AND CHROMATIN STRUCTURE1
  • 1.1. The importance of transcription1
  • 1.2. Chromatin structure and its remodelling2
  • 1.2.1. Chromatin structure and gene regulation2
  • 1.2.2. Chromatin remodelling factors4
  • 1.2.3. Histone modifications5
  • 1.3. DNA sequence elements9
  • 1.3.1. The gene promoter9
  • 1.3.2. Sequences involved in the basic process of transcription10
  • 1.3.3. Sequences involved in regulated transcription11
  • 1.3.4. Sequences which act at a distance15
  • 1.3.5. Negatively acting DNA sequences20
  • 1.3.6. Interaction between factors bound at various sites21
  • 1.4. Conclusions23
  • References24
  • CHAPTER 2. METHODS FOR STUDYING TRANSCRIPTION FACTORS29
  • 2.1. Introduction29
  • 2.2. Methods for studying DNA–protein interactions29
  • 2.2.1. DNA mobility shift assay29
  • 2.2.2. DNAseI footprinting assay33
  • 2.2.3. Methylation interference assay37
  • 2.2.4. In vivo footprinting assay38
  • 2.3. Methods for purifying and/or cloning transcription factors42
  • 2.3.1. Protein purification42
  • 2.3.2. Gene cloning46
  • 2.4. Use of cloned genes51
  • 2.4.1. Domain mapping of transcription factors51
  • 2.4.2. Determining the DNA binding specificity of an uncharacterized factor55
  • 2.4.3. Identification of target genes for transcription factors57
  • 2.5. Conclusions62
  • References63
  • CHAPTER 3. RNA POLYMERASES AND THE BASAL TRANSCRIPTIONAL COMPLEX68
  • 3.1. RNA polymerases68
  • 3.2. The stable transcriptional complex70
  • 3.3. RNA polymerase I71
  • 3.4. RNA polymerase III73
  • 3.5. RNA polymerase II76
  • 3.5.1. Stepwise assembly of the RNA polymerase II basal transcriptional complex76
  • 3.5.2. The RNA polymerase holoenzyme80
  • 3.6. TBP: the universal transcription factor?81
  • 3.7. Transcriptional elongation88
  • 3.8. Conclusions90
  • References90
  • CHAPTER 4. FAMILIES OF DNA BINDING TRANSCRIPTION FACTORS96
  • 4.1. Introduction96
  • 4.2. The homeodomain97
  • 4.2.1. Transcription factors in Drosophila development97
  • 4.2.2. The homeobox98
  • 4.2.3. DNA binding by the helix-turn-helix motif in the homeobox100
  • 4.2.4. Regulation of DNA binding specificity by interactions between different homeobox proteins108
  • 4.2.5. Homeodomain transcription factors in other organisms112
  • 4.2.6. POU proteins114
  • 4.2.7. Pax proteins124
  • 4.3. The two cysteine two histidine Zinc finger126
  • 4.3.1. Transcription factors with the two cysteine two histidine finger126
  • 4.3.2. DNA binding by the two cysteine two histidine finger128
  • 4.4. The multi-cysteine Zinc finger131
  • 4.4.1. Nuclear receptors131
  • 4.4.2. DNA binding by the multi-cysteine zinc finger133
  • 4.5. The basic DNA binding domain142
  • 4.5.1. The leucine zipper and the basic DNA binding domain142
  • 4.5.2. The helix-loop-helix motif and the basic DNA binding domain147
  • 4.5.3. Dimerization of basic DNA binding domain-containing factors149
  • 4.6. Other DNA binding motifs151
  • 4.7. Conclusions152
  • References154
  • CHAPTER 5. ACTIVATION OF GENE EXPRESSION BY TRANSCRIPTION FACTORS161
  • 5.1. Activation domains161
  • 5.2. Nature of activation domains163
  • 5.2.1. Acidic domains163
  • 5.2.2. Glutamine-rich domains166
  • 5.2.3. Proline-rich domains166
  • 5.2.4. Functional relationship of the different activation domains167
  • 5.3. Interaction of activation domains with the basal transcriptional complex168
  • 5.3.1. Activators and the basal transcriptional complex168
  • 5.3.2. Stimulation of factor binding170
  • 5.3.3. Stimulation of factor activity173
  • 5.4. Interaction of activation domains with other regulatory proteins177
  • 5.4.1. The mediator complex177
  • 5.4.2. TAFs180
  • 5.4.3. CBP and other co-activators187
  • 5.4.4. A multitude of targets for transcriptional activators193
  • 5.5. Effect of transcriptional activators on chromatin structure195
  • 5.5.1. Effect of chromatin remodelling factors195
  • 5.5.2. Effect on histone modification203
  • 5.5.3. Transcriptional activation by chromatin structure changes and by stimulation of the basal tra207
  • 5.6. Stimulation of transcriptional elongation212
  • 5.7. Conclusions217
  • References221
  • CHAPTER 6. REPRESSION OF GENE EXPRESSION BY TRANSCRIPTION FACTORS229
  • 6.1. Repression of transcription229
  • 6.2. Indirect repression230
  • 6.2.1. Inhibition of activator binding by masking of its DNA binding site230
  • 6.2.2. Inhibition of activator binding by formation of a non-DNA binding complex235
  • 6.2.3. Quenching of an activator237
  • 6.2.4. Degradation of an activator238
  • 6.3. Direct repression239
  • 6.3.1. Mechanisms of transcriptional repression239
  • 6.3.2. Direct repression by DNA binding transcription factors240
  • 6.3.3. Direct repression by factors binding to the basal transcriptional complex247
  • 6.4. Inhibition by alteration of chromatin structure251
  • 6.4.1. Effect of repressors on chromatin251
  • 6.4.2. Small RNAs and transcriptional inhibition257
  • 6.5. Inhibition of transcriptional elongation259
  • 6.6. Conclusions263
  • References265
  • CHAPTER 7. REGULATION OF TRANSCRIPTION FACTOR SYNTHESIS271
  • 7.1. Transcription factor regulation271
  • 7.2. Regulated synthesis of transcription factors271
  • 7.2.1. The MyoD transcription factor272
  • 7.2.2. Homeobox transcription factors281
  • 7.3. Mechanisms regulating the synthesis of transcription factors294
  • 7.3.1. Regulation of transcription294
  • 7.3.2. Regulation of RNA splicing297
  • 7.3.3. Regulation of translation304
  • 7.4. Conclusions307
  • References308
  • CHAPTER 8. REGULATION OF TRANSCRIPTION FACTOR ACTIVITY312
  • 8.1. Evidence for the regulated activity of transcription factors312
  • 8.2. Regulation by protein–ligand binding314
  • 8.2.1. Examples of regulation by ligand binding314
  • 8.2.2. The nuclear receptors317
  • 8.3. Regulation by protein–protein interactions325
  • 8.3.1. Inhibition of transcription factor activity by protein–protein interaction325
  • 8.3.2. Activation of transcription factors by protein–protein interaction335
  • 8.3.3. Alteration of transcription factor function by protein–protein interaction335
  • 8.4. Regulation by protein modification337
  • 8.4.1. Transcription factor modification337
  • 8.4.2. Phosphorylation337
  • 8.4.3. Acetylation347
  • 8.4.4. Methylation348
  • 8.4.5. Ubiquitination and sumoylation350
  • 8.5. Regulation by protein degradation and processing358
  • 8.6. Role of regulated activity362
  • 8.7. Conclusions364
  • References366
  • CHAPTER 9. TRANSCRIPTION FACTORS AND HUMAN DISEASE373
  • 9.1. Diseases caused by transcription factor mutations373
  • 9.2. Cancer380
  • 9.3. Cellular oncogenes and cancer382
  • 9.3.1. Fos, Jun and AP1382
  • 9.3.2. v-erbA and the thyroid hormone receptor388
  • 9.3.3. The myc oncogene392
  • 9.3.4. Other oncogenic transcription factors399
  • 9.4 Anti-oncogenes and cancer403
  • 9.4.1. Nature of anti-oncogenes403
  • 9.4.2. p53404
  • 9.4.3. The Retinoblastoma protein413
  • 9.4.4. Other anti-oncogenic transcription factors420
  • 9.5. Transcription factors and treatment of human disease425
  • 9.6. Conclusions435
  • References437
  • CHAPTER 10. CONCLUSIONS AND FUTURE PROSPECTS449
  • Index453
  • A453
  • B454
  • C454
  • D456
  • E457
  • F458
  • G459
  • H459
  • I461
  • J462
  • K462
  • L462
  • M463
  • N464
  • O465
  • P465
  • Q467
  • R467
  • S468
  • T469
  • U470
  • V471
  • W471
  • X471
  • Y471
  • Z471
  • Color platesPlate1
Book details
  • Vendor Elsevier S & T
  • SKU 9780123739834R150
  • ISBN-13 9780080561035
  • Author Latchman, David; Latchman, David S.
  • Edition 5th
  • Category Science
  • Subject Genetics & Genomics

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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