Eukaryotic RNA polymerase II has many structural similarities to bacterial RNA polymerase (Figure 6–14). But there are several important differences in the way in which the bacterial and eukaryotic enzymes function, two of which concern us immediately.
1.
While bacterial RNA polymerase requires only a single transcriptioninitiation factor (σ) to begin transcription, eukaryotic RNA polymerases require many such factors, collectively called the general transcription factors.
2.
Eukaryotic transcription initiation must take place on DNA that is packaged into nucleosomes and higher-order forms of chromatin structure (described in Chapter 4), features that are absent from bacterial chromosomes.
Figure 6–13 Directions of transcription along a short portion of a bacterial chromosome. Some genes are transcribed using one DNA strand as a template, while others are transcribed using the other DNA strand. The direction of transcription is determined by the promoter at the beginning of each gene (green arrowheads). This diagram shows approximately 0.2% (9000 base pairs) of the E. coli chromosome. The genes transcribed from left to right use the bottom DNA strand as the template; those transcribed from right to left use the top strand as the template.
RNA Polymerase II Requires a Set of General Transcription Factors
The general transcription factors help to position eukaryotic RNA polymerase correctly at the promoter, aid in pulling apart the two strands of DNA to allow transcription to begin, and release RNA polymerase from the promoter to start its elongation mode. The proteins are “general” because they are needed at nearly all promoters used by RNA polymerase II. They consist of a set of interacting proteins denoted arbitrarily as TFIIA, TFIIB, TFIIC, TFIID, and so on (TFII standing for “transcription factor for polymerase II).” In a broad sense, the eukaryotic general transcription factors carry out functions equivalent to those of the σ factor in bacteria; indeed, portions of TFIIF have the same three-dimensional structure as the equivalent portions of σ.
Figure 6–15 illustrates how the general transcription factors assemble at promoters used by RNA polymerase II, and Table 6–3 summarizes their activities. The assembly process begins when TFIID binds to a short double-helical DNA sequence primarily composed of T and A nucleotides. For this reason, this sequence is known as the TATA sequence, or TATA box, and the subunit of TFIID that recognizes it is called TBP (for TATA-binding protein). The TATA box is typically located 25 nucleotides upstream from the transcription start site. It is not the only DNA sequence that signals the start of transcription (Figure 6–16), but for most polymerase II promoters it is the most important. The binding of TFIID