Harpers

348 / CHAPTER 37site (from −3 to +5) and consists of the general consensussequence TCA +1 G/T T T/C which is similar to theinitiation site sequence per se. (A+1 indicates the firstnucleotide transcribed.) The proteins that bind to Inr inorder to direct pol II binding include TFIID. Promotersthat have both a TATA box and an Inr may be strongerthan those that have just one of these elements. TheDPE has the consensus sequence A/GGA/T CGTG andis localized about 25 bp downstream of the +1 start site.Like the Inr, DPE sequences are also bound by the TAFsubunits of TFIID. In a survey of over 200 eukaryoticgenes, roughly 30% contained a TATA box and Inr,25% contained Inr and DPE, 15% contained all threeelements, while ~30% contained just the Inr.Sequences farther upstream from the start site determinehow frequently the transcription event occurs.Mutations in these regions reduce the frequency oftranscriptional starts tenfold to twentyfold. Typical ofthese DNA elements are the GC and CAAT boxes, sonamed because of the DNA sequences involved. As illustratedin Figure 37–7, each of these boxes binds aprotein, Sp1 in the case of the GC box and CTF (orC/EPB,NF1,NFY) by the CAAT box; both bindthrough their distinct DNA binding domains (DBDs).The frequency of transcription initiation is a consequenceof these protein-DNA interactions and complexinteractions between particular domains of the transcriptionfactors (distinct from the DBD domains—socalledactivation domains; ADs) of these proteins andthe rest of the transcription machinery (RNA polymeraseII and the basal factors TFIIA, B, D, E, F). (Seebelow and Figures 37–9 and 37–10). The protein-DNA interaction at the TATA box involving RNApolymerase II and other components of the basal transcriptionmachinery ensures the fidelity of initiation.Together, then, the promoter and promoter-proximalcis-active upstream elements confer fidelity and frequencyof initiation upon a gene. The TATA box has aparticularly rigid requirement for both position and orientation.Single-base changes in any of these cis elementshave dramatic effects on function by reducingthe binding affinity of the cognate trans factors (eitherTFIID/TBP or Sp1, CTF, and similar factors). Thespacing of these elements with respect to the transcriptionstart site can also be critical. This is particularlytrue for the TATA box Inr and DPE.A third class of sequence elements can either increaseor decrease the rate of transcription initiation of eukaryoticgenes. These elements are called either enhancers orrepressors (or silencers), depending on which effectthey have. They have been found in a variety of locationsboth upstream and downstream of the transcription startsite and even within the transcribed portions of somegenes. In contrast to proximal and upstream promoter elements,enhancers and silencers can exert their effectswhen located hundreds or even thousands of bases awayfrom transcription units located on the same chromosome.Surprisingly, enhancers and silencers can functionin an orientation-independent fashion. Literally hundredsof these elements have been described. In somecases, the sequence requirements for binding are rigidlyconstrained; in others, considerable sequence variation isHFATATADBEpol II–50 –30–10 +10 +30+50Figure 37–9. The eukaryotic basal transcription complex. Formation of the basal transcription complex beginswhen TFIID binds to the TATA box. It directs the assembly of several other components by protein-DNA andprotein-protein interactions. The entire complex spans DNA from position −30 to +30 relative to the initiation site(+1, marked by bent arrow). The atomic level, x-ray-derived structures of RNA polymerase II alone and of TBPbound to TATA promoter DNA in the presence of either TFIIB or TFIIA have all been solved at 3 Å resolution. Thestructure of TFIID complexes have been determined by electron microscopy at 30 Å resolution. Thus, the molecularstructures of the transcription machinery are beginning to be elucidated. Much of this structural information isconsistent with the models presented here.