MBMB 451A Section One - Fall 2006
Regulation of TranscriptionI. Basal versus activated transcription for mRNA genes A. General transcription factor (TF) vs. promoter-specific TF 1. general TFs are required by all mRNA genes a. an absolute requirement b. transcription can occur alone with these factors is by definition the basal level of transcription 2. promoter-specific TFs are different for each gene 3. the promoter-specific TFs are required for maximal level of transcription or for activated transcription (induction) B. a third state is that of a repressed state II. Question of Activation A. diversity of response - combinatorial effect 1. properities of response elements (RE) 2. relatedness of RE and enhancers 3. trans acting factors induction: heat shock, heavy metals, viral infection, growth factors, steroids 4. greater multiplicity with combinatorial approach B. Master gene regulatory proteins 1. response elements shared 2. example of homeodomains C. regulating the activity of the transcription factors figure D. mechanisms of activation 1. recruitment 2. conformational change 3. covalent modification III. DNA binding domains A. Steroid receptors 1. Ligand mediated activation 2. Functional Domains a. DNA binding b. ligand binding - hormone c. activation domain 3. Two classes a. form homodimers: bind consensus half site (TGTTCT, except for ER is TGACCT) b. form heterodimers: bind half sites of TGACCT, direct repeats c. spacing of the half sites is crucial for the degree of specificity B. Zinc fingers 1. Cys2-His2 fingers: Cys - X2-4 -Cys - X3 - Phe - X5 - Leu - X2 - His - X - His figures 34-54 a & b and 34-55 a. example is TFIIIA has 9 Zn finger repeat b. typically the number of fingers range from 2-9 c. can be involved in binding to RNA d. not all Zn fingers are used to bind DNA, nor are they always part of a transcription factor 2. Cys2-Cys2 fingers: Cys - X2 - Cys - X13 - Cys - X2 - Cys figure 34-56 a. found in steroid receptors b. typically nonrepetitive c. binding sites are short palindromes d. bind as dimers 3. Binuclear Cys6 finger: Gal4 DNA binding domains figure 34-57 C. Leucine zippers - dimer formation figure 34-58 1. brings 2 DNA binding domains in close juxtaposition example is Gal4 see figure 34-57 2. amphipathic alpha helices with Leu residues on one face Leu repeats every 7 amino acid 3. interface forms a coiled coil D. bZIP example is GCN5 figure 34-59 1. basic region attached to a leucine zipper 2. is a dimer kept together by the leucine zipper 3. an alpha helic containing basic residues contacts the major groove of DNA 4. contacts are made twith the portion of the bases exposed in the major groove and some phosphate backbone contacts E. bHLH figure 34-60 1. basic helix loop helix motif 2. positively charged alpha helix binds to major groove 3. two other alpha helices form a four helix bundle in dimer 4. many will also contain a leucine zipper F. Dimer formation regulates the activity of the transcription factor good example IV. Activation Domains A. Acidic activators - example of Gal4p B. Glutamine rich domain C. Proline rich domain V. Transcription Elongation A. General 1. in vivo rates are 1200-2000 nucleotides/min 2. in vitro rates are 100-300 nucleotides/min 3. elongation is not a monotonic continuous process a. there are strong pause sites b. effects of chromatin on process 4. pausing versus arrest (definition of) B. Negative elongation factors (N-TEFs) 1. DSIF 2. factor 2 C. Positive elongation factors (P-TEFs) 1. prevent sequence dependent arrest (i.e. TFIIS or SII) nucleolytic cleavage/ backtracking 2. catalytic activity (TFIIF, elongin, ELL complex) 3. regulates the rate of elongation through chromatin (FACT)
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Last updated on September 14, 2006 .
