EUKARYOTIC TRANSCRIPTION FACTORS
1 DNA SEQUENCES, TRANSCRIPTION FACTORS AND CHROMATIN STRUCTURE 1 1 THE IMPORTANCE OF TRANSCRIPTION 1 2 CHROMATIN STRUCTURE AND ITS REMODELLING 1 2 1 CHROMATIN STRUCTURE AND GENE REGULATION 1 2 2 CHROMATIN REMODELLING FACTORS 1 2 3 HISTONE MODIFICATIONS 1 3 DNA SEQUENCE ELEMENTS 1 3 1 THE GENE PROMOTER 1 3 2 SEQUENCES INVOLVED IN THE BASIC PROCESS OF TRANSCRIPTION 1 3 3 SEQUENCES INVOLVED IN REGULATED TRANSCRIPTION 1 3 4 SEQUENCES WHICH ACT AT A DISTANCE 1 3 5 NEGATIVELY ACTING DNA SEQUENCES 1 3 6 INTERACTION BETWEEN FACTORS BOUND AT VARIOUS SITES 1 4 CONCLUSIONS REFERENCES 2 METHODS FOR STUDYING TRANSCRIPTION FACTORS 2 1 INTRODUCTION 2 2 METHODS FOR STUDYING DNA–PROTEIN INTERACTIONS 2 2 1 DNA MOBILITY SHIFT ASSAY 2 2 2 DNASEI FOOTPRINTING ASSAY 2 2 3 METHYLATION INTERFERENCE ASSAY 2 2 4 IN VIVO FOOTPRINTING ASSAY C O N T E N T S 2 3 METHODS FOR PURIFYING AND/OR CLONING TRANSCRIPTION FACTORS 2 3 1 PROTEIN PURIFICATION 2 3 2 GENE CLONING 2 4 USE OF CLONED GENES 2 4 1 DOMAIN MAPPING OF TRANSCRIPTION FACTORS 2 4 2 DETERMINING THE DNA BINDING SPECIFICITY OF AN UNCHARACTERIZED FACTOR 2 4 3 IDENTIFICATION OF TARGET GENES FOR TRANSCRIPTION FACTORS 2 5 CONCLUSIONS 3 RNA POLYMERASES AND THE BASAL TRANSCRIPTIONAL COMPLEX 3 1 RNA POLYMERASES 3 2 THE STABLE TRANSCRIPTIONAL COMPLEX 3 3 RNA POLYMERASE I 3 4 RNA POLYMERASE III 3 5 RNA POLYMERASE II 3 5 1 STEPWISE ASSEMBLY OF THE RNA POLYMERASE II BASAL TRANSCRIPTIONAL COMPLEX 3 5 2 THE RNA POLYMERASE HOLOENZYME 3 6 TBP: THE UNIVERSAL TRANSCRIPTION FACTOR? 3 7 TRANSCRIPTIONAL ELONGATION 3 8 CONCLUSIONS 4 FAMILIES OF DNA BINDING TRANSCRIPTION FACTORS 4 1 INTRODUCTION 4 2 THE HOMEODOMAIN 4 2 1 TRANSCRIPTION FACTORS IN DROSOPHILA DEVELOPMENT 4 2 2 THE HOMEOBOX 4 2 3 DNA BINDING BY THE HELIX-TURN-HELIX MOTIF IN THE HOMEOBOX 4 2 4 REGULATION OF DNA BINDING SPECIFICITY BY INTERACTIONS BETWEEN DIFFERENT HOMEOBOX PROTEINS 4 2 5 HOMEODOMAIN TRANSCRIPTION FACTORS IN OTHER ORGANISMS 4 2 6 POU PROTEINS 4 2 7 PAX PROTEINS 4 3 THE TWO CYSTEINE TWO HISTIDINE ZINC FINGER 4 3 1 TRANSCRIPTION FACTORS WITH THE TWO CYSTEINE TWO HISTIDINE FINGER 4 3 2 DNA BINDING BY THE TWO CYSTEINE TWO HISTIDINE FINGER 4 4 THE MULTI-CYSTEINE ZINC FINGER 4 4 1 NUCLEAR RECEPTORS 4 4 2 DNA BINDING BY THE MULTI-CYSTEINE ZINC FINGER 4 5 THE BASIC DNA BINDING DOMAIN 4 5 1 THE LEUCINE ZIPPER AND THE BASIC DNA BINDING DOMAIN 4 5 2 THE HELIX-LOOP-HELIX MOTIF AND THE BASIC DNA BINDING DOMAIN 4 5 3 DIMERIZATION OF BASIC DNA BINDING DOMAIN-CONTAINING FACTORS 4 6 OTHER DNA BINDING MOTIFS 4 7 CONCLUSIONS 5 ACTIVATION OF GENE EXPRESSION BY TRANSCRIPTION FACTORS 5 1 ACTIVATION DOMAINS 5 2 NATURE OF ACTIVATION DOMAINS 5 2 1 ACIDIC DOMAINS 5 2 2 GLUTAMINE-RICH DOMAINS 5 2 3 PROLINE-RICH DOMAINS 5 2 4 FUNCTIONAL RELATIONSHIP OF THE DIFFERENT ACTIVATION DOMAINS 5 3 INTERACTION OF ACTIVATION DOMAINS WITH THE BASAL TRANSCRIPTIONAL COMPLEX 5 3 1 ACTIVATORS AND THE BASAL TRANSCRIPTIONAL COMPLEX 5 3 2 STIMULATION OF FACTOR BINDING 5 3 3 STIMULATION OF FACTOR ACTIVITY 5 4 INTERACTION OF ACTIVATION DOMAINS WITH OTHER REGULATORY PROTEINS 5 4 1 THE MEDIATOR COMPLEX 5 4 2 TAFS 5 4 3 CBP AND OTHER CO-ACTIVATORS 5 4 4 A MULTITUDE OF TARGETS FOR TRANSCRIPTIONAL ACTIVATORS 5 5 EFFECT OF TRANSCRIPTIONAL ACTIVATORS ON CHROMATIN STRUCTURE 5 5 1 EFFECT OF CHROMATIN REMODELLING FACTORS 5 5 2 EFFECT ON HISTONE MODIFICATION 5 5 3 TRANSCRIPTIONAL ACTIVATION BY CHROMATIN STRUCTURE CHANGES AND BY STIMULATION OF THE BASAL TRANSCRIPTIONAL COMPLEX 5 6 STIMULATION OF TRANSCRIPTIONAL ELONGATION 5 7 CONCLUSIONS 6 REPRESSION OF GENE EXPRESSION BY TRANSCRIPTION FACTORS 6 1 REPRESSION OF TRANSCRIPTION 6 2 INDIRECT REPRESSION 6 2 1 INHIBITION OF ACTIVATOR BINDING BY MASKING OF ITS DNA BINDING SITE 6 2 2 INHIBITION OF ACTIVATOR BINDING BY FORMATION OF A NON-DNA BINDING COMPLEX 6 2 3 QUENCHING OF AN ACTIVATOR 6 2 4 DEGRADATION OF AN ACTIVATOR 6 3 DIRECT REPRESSION 6 3 1 MECHANISMS OF TRANSCRIPTIONAL REPRESSION 6 3 2 DIRECT REPRESSION BY DNA BINDING TRANSCRIPTION FACTORS 6 3 3 DIRECT REPRESSION BY FACTORS BINDING TO THE BASAL TRANSCRIPTIONAL COMPLEX 6 4 INHIBITION BY ALTERATION OF CHROMATIN STRUCTURE 6 4 1 EFFECT OF REPRESSORS ON CHROMATIN 6 4 2 SMALL RNAS AND TRANSCRIPTIONAL INHIBITION 6 5 INHIBITION OF TRANSCRIPTIONAL ELONGATION 6 6 CONCLUSIONS 7 REGULATION OF TRANSCRIPTION FACTOR SYNTHESIS 7 1 TRANSCRIPTION FACTOR REGULATION 7 2 REGULATED SYNTHESIS OF TRANSCRIPTION FACTORS 7 2 1 THE MYOD TRANSCRIPTION FACTOR 7 2 2 HOMEOBOX TRANSCRIPTION FACTORS 7 3 MECHANISMS REGULATING THE SYNTHESIS OF TRANSCRIPTION FACTORS 7 3 1 REGULATION OF TRANSCRIPTION 7 3 2 REGULATION OF RNA SPLICING 7 3 3 REGULATION OF TRANSLATION 7 4 CONCLUSIONS 8 REGULATION OF TRANSCRIPTION FACTOR ACTIVITY 8 1 EVIDENCE FOR THE REGULATED ACTIVITY OF TRANSCRIPTION FACTORS 8 2 REGULATION BY PROTEIN–LIGAND BINDING 8 2 1 EXAMPLES OF REGULATION BY LIGAND BINDING 8 2 2 THE NUCLEAR RECEPTORS 8 3 REGULATION BY PROTEIN–PROTEIN INTERACTIONS 8 3 1 INHIBITION OF TRANSCRIPTION FACTOR ACTIVITY BY PROTEIN–PROTEIN INTERACTION 8 3 2 ACTIVATION OF TRANSCRIPTION FACTORS BY PROTEIN–PROTEIN INTERACTION 8 3 3 ALTERATION OF TRANSCRIPTION FACTOR FUNCTION BY PROTEIN–PROTEIN INTERACTION 8 4 REGULATION BY PROTEIN MODIFICATION 8 4 1 TRANSCRIPTION FACTOR MODIFICATION 8 4 2 PHOSPHORYLATION 8 4 3 ACETYLATION 8 4 4 METHYLATION 8 4 5 UBIQUITINATION AND SUMOYLATION 8 5 REGULATION BY PROTEIN DEGRADATION AND PROCESSING 8 6 ROLE OF REGULATED ACTIVITY 8 7 CONCLUSIONS 9 TRANSCRIPTION FACTORS AND HUMAN DISEASE 9 1 DISEASES CAUSED BY TRANSCRIPTION FACTOR MUTATIONS 9 2 CANCER 9 3 CELLULAR ONCOGENES AND CANCER 9 3 2 V-ERBA AND THE THYROID HORMONE RECEPTOR 9 3 3 THE MYC ONCOGENE 9 3 4 OTHER ONCOGENIC TRANSCRIPTION FACTORS 9 4 ANTI-ONCOGENES AND CANCER 9 4 1 NATURE OF ANTI-ONCOGENES 9 4 3 THE RETINOBLASTOMA PROTEIN 9 4 4 OTHER ANTI-ONCOGENIC TRANSCRIPTION FACTORS 9 5 TRANSCRIPTION FACTORS AND TREATMENT OF HUMAN DISEASE 9 6 CONCLUSIONS 10 CONCLUSIONS AND FUTURE PROSPECTS