Eukaryotic Transcription Factors

DNA sequences, transcription factors and chromatin structureThe importance of transcriptionChromatin structure and its remodelling Chromatin structure and gene regulationChromatin remodelling factorsHistone acetylationDNA sequence elementsThe gene promoterSequences involved in the basic process of transcription Sequences involved in regulated transcriptionSequences which act at a distanceNegatively acting DNA sequencesInteraction between factors bound at various sitesConclusionsReferencesMethods for studying transcription factorsIntroductionMethods for studying DNA-protein interactionsDNA mobility shift assayDNaseI footprinting assayMethylation interference assayIn vivo Footprinting assayMethods for purifying and/or cloning transcription factorsProtein purificationGene cloningUse of cloned genesDomain mapping of transcription factorsDetermining the DNA binding specificity of an uncharacterised factorIdentification of target genes for transcription factorsConclusionsReferencesTranscription factors and constitutive transcriptionRNA polymerasesThe stable transcriptional complexRNA polymerase IRNA polymerase IIIRNA polymerase IIStepwise assembly of the RNA polymerase II basal transcriptional complexThe RNA polymerase holoenzymeTBP, The universal transcription factor?ConclusionsReferencesFamilies of DNA binding transcription factorsIntroductionThe homeodomainTranscription factors in Drosophila developmentThe homeoboxDNA binding by the helix-turn-helix motif in the homeoboxRegulation of DNA binding specificity by interaction between differenthomeobox proteinsHomeodomain transcription factors in other organismsPOU proteinsPax proteinsThe two cysteine two histidine fingerTranscription factors with the two cysteine two histidine fingerDNA binding by the two cysteine two histidine fingerThe multi-cysteine fingerSteroid receptorsDNA binding by the multi-cysteine zinc fingerThe basic DNA binding domainThe leucine zipper and the basic DNA binding domainThe helix-loop-helix motif and the basic DNA binding domainDimerisation of basic DNA binding domain-containing factorsOther DNA-binding motifsConclusionsReferencesActivation of gene expression by transcription factorsActivation domainsNature of activation domainsAcidic domainsGlutamine-rich domainsProline-rich domainsFunctional relationship of the different activation domainsInteraction of activation domains with the basal transcriptional complexActivators and the basal transcriptional complexStimulation of factor bindingStimulation of factor activityInteraction of activation domains with other regulatory proteinsThe mediator complexTAFsCBP and other co-activatorsA multitude of targets for transcriptional activatorsOther targets for transcriptional activatorsModulation of chromatin structureStimulation of transcriptional elongationConclusionsRepression of gene expression by transcription factorsRepression of transcriptionIndirect repressionInhibition of activator binding by masking of its DNA binding siteInhibition of activator binding by formation of a non-DNA bindingcomplexQuenching of an activatorDegradation of an activatorDirect repressionMechanisms of transcriptional repressionDirect repression by DNA binding transcription factorsDirect repression by factors binding to the basal transcriptional complexOther targets for transcriptional repressorsModulation of chromatin structureInhibition of transcriptional elongationConclusionsReferencesRegulation of transcription factor synthesisTranscription factor regulationRegulated synthesis of transcription factorsThe MyoD transcription factorHomeobox transcription factorsMechanisms regulating the synthesis of transcription factorsRegulation of transcriptionRegulation of RNA splicingRegulation of translationConclusionsRegulation of transcription factorEvidence for the regulated activity of transcription factorsRegulation by protein-ligand bindingExamples of regulation by ligand bindingThe nuclear receptorsRegulation by protein-protein interactionsInhibition of transcription factor activity by protein-protein interactionActivation of transcription factors by protein-protein interactionAlteration of transcription factor function by protein-protein interactionRegulation by protein modificationTranscription factor modificationPhosphorylationAcetylationMethylationUbiquitinationRegulation by protein degradation and processingRole of regulated activityConclusionsTranscription factors and human diseaseDiseases caused by transcription factor mutationsCancerCellular oncogenes and cancerFos, Jun and AP1v-erbA and the thyroid hormone receptorThe myc oncogeneOther oncogenic transcription factorsAnti-oncogenes and cancerNature of anti-oncogenesp53The Retinoblastoma proteinOther anti-oncogenic transcription factors.ConclusionsReferencesConclusions and future prospects