Chapter 25: Regulating Eukaryotic Transcription

Chapter 25: Regulating Eukaryotic Transcription • At least 5 potential gene expression control points Gene expression is controlled: • principally at the initiation of transcription • rare for the subsequent stages to be used to determine whether a gene is expressed, Activation of gene structure Initiation of transcription • control of processing may be used to determine which form of a gene is represented in mRNA. Processing the transcript Transport to the cytoplasm Translation of mRNA 25.2 There Are Several Types of Transcription Factors • The basal apparatus determines: • the startpoint for transcription. • A basal factor is: • Activators determine: • the frequency of transcription. – a transcription factor required by RNA polymerase II to form the initiation complex at all promoters. – Factors are identified as TFIIX, where X is a letter. • An activator is: – a protein that stimulates the expression of a gene, – typically by acting at a promoter to stimulate RNA polymerase binding. – the sequence to which it binds in the promoter is called a response element. • A response element is: – a sequence in a eukaryotic promoter or enhancer – is recognized by a specific transcription factor. • Coactivators are: – factors required for transcription that do not bind DNA – but are required for (DNA-binding) activators to interact with the basal transcription factors. • Activators work by: • making protein–protein contacts with the basal factors. • Activators may work: • via coactivators. • local chromatin structure: •May be regulated or changed 1 25.3 Independent Domains Bind DNA and Activate Transcription DNA-binding and activating functions in a transcription factor may be in independent domains of the protein. • DNA-binding activity and transcription activation – are carried out by independent domains of an activator. • The DNA-binding domain determines – specificity for the target promoter or enhancer. • The role of the DNA-binding domain is to – bring the transcription activation domain into the vicinity of the promoter. 25.4 Activators Interact with the Basal Apparatus • An activator that works directly has – a DNA-binding domain – and an activating domain. • An activator that does not have an activating domain – may work by binding a coactivator that has an activating domain. • Several factors in the basal apparatus – are targets with which activators or coactivators interact. • RNA polymerase may be associated with – various alternative sets of transcription factors in a holoenzyme complex. – • Repression is usually achieved by – affecting chromatin structure, – but there are repressors that act by binding to specific promoters. 2 25.5 Response Elements Are Recognized by Activators Common Response Elements That Are Recognized by Activators • The heat shock response element (HSE) is – a sequence in a promoter or enhancer that is used to activate a gene by an activator induced by heat shock. • Response elements may be located in promoters or enhancers. • Each response element is recognized by a specific activator. • A promoter may have many response elements, which may activate transcription independently or in certain combinations. • The glucocorticoid response element (GRE) is – a sequence in a promoter or enhancer that is recognized by the glucocorticoid receptor, which is activated by glucocorticoid steroids. • The serum response element (SRE) is – a sequence in a promoter or enhancer that is activated by transcription factor(s) induced by treatment with serum. – This activates genes that stimulate cell growth. • Heat shock genes are a set of loci that are – activated in response to an increase in temperature (and other abuses to the cell). – All organisms have heat shock genes. – Their products usually include chaperones that act on denatured proteins. 3 25.6 There Are Many Types of DNA-Binding Domains • Activators are classified according to the type of DNA-binding domain. • Members of the same group have sequence variations of a specific motif that confer specificity for individual target sites. 25.6 There Are Many Types of DNA-Binding Domains • The zinc finger is Transcription factors are activated in several ways • The activity of a regulatory transcription factor may be controlled by – a DNA-binding motif that typifies a class of transcription factor (TF). • Steroid receptors are – synthesis of protein – TFs that are activated by binding of a steroid ligand. • The helix-turn-helix motif describes – an arrangement of two α-helices that form a site that binds to DNA, – one fitting into the major groove of DNA and other lying across it. • The homeodomain is – a DNA-binding motif that typifies a class of TFs. – The DNA sequence that codes for it is called the homeobox. – covalent modification of protein – ligand binding – or binding of inhibitors that sequester the protein or affect its ability to bind to DNA. • The helix-loop-helix (HLH) motif is – responsible for dimerization of a class of TFs called HLH proteins. – has a basic DNA-binding sequence close to the dimerization motif. • The leucine zipper is – a dimerization motif adjacent to a basic DNA-binding region 4 25.7 A Zinc Finger Motif Is a DNA-Binding Domain • A zinc finger is a loop of ~23 amino acids that – protrudes from a zinc-binding site formed by His and Cys amino acids. • A zinc finger protein usually has multiple zinc fingers. • The C-terminal part of each finger forms – an α-helix that binds one turn of the major groove of DNA. • Some zinc finger proteins bind – RNA instead of or as well as DNA. Transcription factor SP1 has a series of three zinc fingers, each with a characteristic pattern of cysteine and histidine residues that constitute the zinc-binding site. (Cys2/His2) 5 25.8 Some Steroid Hormone Receptors Are Transcription Factors • Steroid receptors are examples of ligand-responsive activators that are activated by – binding a steroid (or other related molecules). • There are separate DNA-binding and ligand-binding domains. • A variety of hydrophobic ligands activate these transcription factors • Several types of hydrophobic small molecules activate these transcription factors. 6