General Transcription factors:
The structure of RNA polymerase II reveals specific sites for DNA binding, whereas the promoter region contains elements to which the enzyme binds to. But how exactly does the enzyme actually reach its destination onto the DNA to initiate transcription? This role is taken on by the eukaryotic general transcription factors which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH. TFII stands for transcription factor of RNA polymerase II and the letter that follows represents a different type of factor with its own function. The general transcription factors aid in recruiting RNA polymerase II to the core promoter region and prepare the enzyme to initiate transcription by forming the pre-initiation complex. It is thought that this complex not only helps RNA polymerase II leave the promoter but ultimately it serves to evolve into a complex necessary for the elongation.
TFIID is a protein complex that contains both a TATA box-binding protein (TBP) and TBP-associated factors (TAFs). The TBP resembles a saddle-like structure that binds the TATA box region of the promoter. This causes the bending and possible unwinding of the DNA, which is necessary to initiate transcription. In organisms that contain TATA box-containing genes, the TBP can locate and bind to the TATA box. However, in TATA box-less organisms, TAF’s helps the TBP select its binding location on the core promoter region. In both TATA box-containing and TATA box-less organisms, TAF’s facilitate the binding of the TBP and thus increase transcriptional efficiency.
TFIIA binds to the TBP and interacts with a site within the TATA box region (1). This protein factor serves to stabilize the interactions between the DNA and the TBP. TFIIA also binds activators and displaces repressors, which is necessary for transcriptional activation. Activators and repressors control the level of expression for a certain gene by either promoting (activators) or inhibiting (repressors) the binding of RNA polymerase.
TFIIB also serves to stabilize TBP-DNA interactions (6). This protein factor binds to the TBP, but interacts with the TATA box region at a site further downstream (closer to the start site) than TFIIA does. TFIIB serves as an appropriate spacer or linker between the TBP and RNA Polymerase II allowing enzyme’s catalytic site to line up with the transcription start site on the DNA.
TFIIF binds to a subunit region of RNA polymerase II known as RAP30. As a sub-complex, TFIIF then causes RNA polymerase II to bind the TBP, which positions the enzyme at its appropriate location to initiate transcription.
TFIIE binds to the promoter-bound complex after RNA polymerase II has bound. This protein factor is thought to recruit TFIIH and stimulate several of its activities. TFIIE may also serve in stabilizing the DNA double helix in its unwound state, which is necessary for transcription initiation.
TFIIH consists of two sub-complexes: core TFIIH and the cyclin/Cdk sub-complex (1). When TFIIH binds to the promoter-bound complex, it displays two main functions: ATP-dependent helicase activity and CTD-kinase activity. Two subunits of core TFIIH, XPB/ERCC3 and XPD/ERCC2, perform helicase activity, which unwinds the DNA double helix and prepares it for initiation. The cyclin/Cdk sub-complexes perform CTD-kinase activity by phosphorylating the CTD of Rpb1 in RNA polymerase II. As explained above, Rpb1 in its phosphorylated state causes the enzyme to move from the initiation stage to the elongation stage of transcription.