RNA
Polymerase II Transcription
Initiation complex - All of the protein-coding genes in eukaryotes are transcribed by RNA polymerase II (pol II). This enzyme also transcribes some of the small nuclear RNAs involved in splicing (see here). Like other RNA polymerases, pol II is a complex, multisubunit enzyme, but not even its numerous subunits are sufficient to allow pol II to initiate transcription on a eukaryotic promoter. To form a minimal complex capable of initiation, at least five additional protein factors are needed Figure 28.24 and listed in Table 28.4. The minimal unit involves the TATA binding protein, (TBP), but in vivo formation of the complex probably always uses TFIID, a multi-subunit structure incorporating both TBP and TATA binding associated factors (TAFs).
Control Elements - A DNA sequence that binds a transcription factor is called a control element. The function of the TATA control element appears to be to fix the starting point for transcription. But eukaryotic pol II promoters contain much more complex and diverse control elements, a few of which are listed in Table 28.5. Because the transcription of genes for proteins must be both tissue specific and developmentally specific, it requires a great deal of regulation. In some cases, transcription must also respond to special signal molecules like hormones. It is common to find, upstream from the TATA box, promoter sequences that bind a variety of trans-acting factors. These are proteins synthesized on other genes that enhance or repress the transcription of the gene in question. The control elements shown are the general elements listed in Table 28.5.
Enhancers - Often, trans-acting factors binding at sequences far removed from the promoter itself--by as much as several kilobase pairs-can influence transcription. Such sequences are called enhancers, and their mode of action appears to involve DNA looping, perhaps mediated by nucleosomes, which can bring enhancer-bound proteins into close physical contact with proteins bound to the promoter. Some of the transcription factors shown in Table 28.4 can bind in either promoter or enhancer regions. The trans-acting factors tend to fall into a small number of classes, each defined by the kind of structural domain that interacts with the DNA. Schematic drawings of three of the better-known types are shown in Figure 28.23.
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