Eukaryotic Transcription Factors / Edition 4

Preface
Acknowledgements
List of Tables
DNA sequences, transcription factors and chromatin structure
The importance of transcription
Chromatin structure and its remodelling
Chromatin structure and gene regulation
Chromatin remodelling factors
Histone acetylation
DNA sequence elements
The gene promoter
Sequences involved in the basic process of transcription
Sequences involved in regulated transcription
Sequences which act at a distance
Negatively acting DNA sequences
Interaction between factors bound at various sites
Conclusions
References
Methods for studying transcription factors
Introduction
Methods for studying DNA-protein interactions
DNA mobility shift assay
DNaseI footprinting assay
Methylation interference assay
In vivo Footprinting assay
Methods for purifying and/or cloning transcription factors
Protein purification
Gene cloning
Use of cloned genes
Domain mapping of transcription factors
Determining the DNA binding specificity of an uncharacterised factor
Identification of target genes for transcription factors
Conclusions
References
Transcription factors and constitutive transcription
RNA polymerases
The stable transcriptional complex
RNA polymerase I
RNA polymerase III
RNA polymerase II
Stepwise assembly of the RNA polymerase II basal transcriptional complex
The RNA polymerase holoenzyme
TBP, The universal transcription factor?
Conclusions
References
Families of DNA binding transcription factors
Introduction
The homeodomain
Transcription factors in Drosophila development
The homeobox
DNA binding by the helix-turn-helix motif in the homeobox
Regulation of DNA binding specificity by interaction between different homeobox proteins
Homeodomain transcription factors in other organisms
POU proteins
Pax proteins
The two cysteine two histidine finger
Transcription factors with the two cysteine two histidine finger
DNA binding by the two cysteine two histidine finger
The multi-cysteine finger
Steroid receptors
DNA binding by the multi-cysteine zinc finger
The basic DNA binding domain
The leucine zipper and the basic DNA binding domain
The helix-loop-helix motif and the basic DNA binding domain
Dimerisation of basic DNA binding domain-containing factors
Other DNA-binding motifs
Conclusions
References
Activation of gene expression by transcription factors
Activation domains
Nature of activation domains
Acidic domains
Glutamine-rich domains
Proline-rich domains
Functional relationship of the different activation domains
Interaction of activation domains with the basal transcriptional complex
Activators and the basal transcriptional complex
Stimulation of factor binding
Stimulation of factor activity
Interaction of activation domains with other regulatory proteins
The mediator complex
TAFs
CBP and other co-activators
A multitude of targets for transcriptional activators
Other targets for transcriptional activators
Modulation of chromatin structure
Stimulation of transcriptional elongation
Conclusions
Repression of gene expression by transcription factors
Repression of transcription
Indirect repression
Inhibition of activator binding by masking of its DNA binding site
Inhibition of activator binding by formation of a non-DNA binding complex
Quenching of an activator
Degradation of an activator
Direct repression
Mechanisms of transcriptional repression
Direct repression by DNA binding transcription factors
Direct repression by factors binding to the basal transcriptional complex
Other targets for transcriptional repressors
Modulation of chromatin structure
Inhibition of transcriptional elongation
Conclusions
References
Regulation of transcription factor synthesis
Transcription factor regulation
Regulated synthesis of transcription factors
The MyoD transcription factor
Homeobox transcription factors
Mechanisms regulating the synthesis of transcription factors
Regulation of transcription
Regulation of RNA splicing
Regulation of translation
Conclusions
Regulation of transcription factor
Evidence for the regulated activity of transcription factors
Regulation by protein-ligand binding
Examples of regulation by ligand binding
The nuclear receptors
Regulation by protein-protein interactions
Inhibition of transcription factor activity by protein-protein interaction
Activation of transcription factors by protein-protein interaction
Alteration of transcription factor function by protein-protein interaction
Regulation by protein modification
Transcription factor modification
Phosphorylation
Acetylation
Methylation
Ubiquitination
Regulation by protein degradation and processing
Role of regulated activity
Conclusions
Transcription factors and human disease
Diseases caused by transcription factor mutations
Cancer
Cellular oncogenes and cancer
Fos, Jun and AP1
v-erbA and the thyroid hormone receptor
The myc oncogene
Other oncogenic transcription factors
Anti-oncogenes and cancer
Nature of anti-oncogenes p53
The Retinoblastoma protein
Other anti-oncogenic transcription factors.
Conclusions
References
Conclusions and future prospects
Index