The general transcription factor (GTF) is required for RNA polymerase II to initiate transcription in eukaryotes. Many of these universal transcription factors do not actually bind DNA, but rather are part of a large transcriptional pre-activation complex that interacts directly with RNA polymerase. The most common GTFs are TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH.
The promoter of many genes transcribed by polymerase II contains a sequence similar to TATAA 25 to 30 nucleotides upstream of the transcription initiation site. This sequence is called the TATA box and the first step in the formation of a transcriptional complex is the binding of the universal transcription factor TFIID. TFIID is a multiprotein complex in which only one polypeptide, the TATA binding protein (TBP), binds to the TATA box. The TATA binding protein specifically binds to the TATAA consensus sequence and about 10 other polypeptides, called TBP related factors.
Figure 1. Crystal structure of TFIID
TFIIA is one of the general transcription factors that bind to the TBP subunit of TFIID and enhance the binding of TFIID to the TATA box, stabilizing the TFIID-DNA complex. The interaction of TFIIA with TBP promotes the formation and stabilization of the pre-initiation complex and also leads to the elimination of negative (inhibitory) factors that may bind to TBP and interfere with the formation of the pre-initiation complex. It appears that the binding of TFIIA to TFIID prevents the binding of inhibitory factors, and thus the formation of transcriptional complexes continues to bind to other transcription factors.
Binding of the TFIID to the TATA box is followed by the recruitment of another transcription factor, TFIIB, which binds to the TATA binding protein (TBP) and the DNA sequence present upstream of the TATA box in some promoters. TFIIB interacts with the TBP subunit of TFIID and the RPB1 subunit of RNA polymerase II for protein-protein interactions. TFIIB acts as a bridge for RNA polymerase II, which binds to the TNP-TFIIB complex with the third factor TF1IF.
Figure 2. Crystal structure of TFIIB
TFIIF is one of several transcription factors required to form an RNA polymerase II pre-priming complex. When the enzyme has been combined with any other transcription factor, TFIIF binds to RNA polymerase II, thereby preventing it from contacting the DNA outside the promoter. In addition, TFIIF stabilizes RNA polymerase II upon exposure to TBP and TFIIB.
TFIIE is another transcription factor which is required to form the RNA polymerase II preinitiation complex. Following recruitment of RNA polymerase II to the promoter, the binding of two additional factors i.e., TFIIE and TFIIH is required for transcription initiation. TFIIE is thought to be involved in DNA melting at the promoter: it contains a zinc ribbon motif that can bind single stranded DNA.
TFIIH is a multi-subgene that plays two important roles in the formation of RNA polymerase II transcription complexes. It contains helicase and kinase activity. The two subunits of TFIIH (XPB and XPD proteins) are helicases that unwind DNA around the start site. Another subunit of TFIIH has protein kinase activity, so it phosphorylates repeats present in the C-terminal domain of the largest subunit of RNA polymerase II. The polymerase II C-terminal domain (CTD) consists of a 7 amino acid sequence repeat with the consensus sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser (replicated 27 times in yeast and 52 times in humans) composition. Phosphorylation of these amino acids releases the polymerase from binding to the pro-in vitro complex and leads to the recruitment of other proteins that allow the polymerase to initiate transcription and begin to synthesize a growing mRNA chain.