The nuclei of eukaryotic cells contain three RNA polymerases (designated I, II and III). These enzymes catalyze the formation of the phosphodiester bond that links nucleotides together to form a linear chain. RNA polymerase moves stepwise along the DNA, unwinding the DNA helix just ahead of the active site for polymerization, to expose a new region of the template strand for complementary base pairing. In this way, the growing RNA chain is extended one nucleotide at a time in the 5' to 3' direction. Each eukaryotic RNA polymerase catalyzes transcription of genes encoding different classes of RNA. RNA polymerase II catalyzes transcription of all protein-coding genes; it functions in the production of mRNAs. RNA Polymerase II also produces four snRNAs (small nuclear RNAs) that take part in RNA splicing.
RNA polymerase II does not directly recognize core promoter sequences. The first step in complex formation is binding of the factor TFIID to a region that extends upstream from the TATA sequence. TFIID is a complex made up of the TBP (TATA binding protein), a small protein of ~30kD and at least 12 TBP-associated factors (TAF). TBP is a sequence specific protein and has a saddle-like shape that wraps partially around the double helix, forming a platform onto which the remainder of the initiation complex can be assembled. TAFs assist in attachment of TFIID to the TATA box. After TFIID has attached to the core promoter, the pre-initiation complex (PIC) is formed by attachment of the remaining general transcription factors. These factors bind to the complex in the order TFIIA, TFIIB, TFIIF/RNA polymerase II, TFIIE and TFIIH. The assembly involves a complex set of interactions of which three events are particularly important: (1) Attachment of TBP which induces the formation of a bend in DNA in the region of the TATA Box, (2) The bend provides a recognition structure for TFIIB, which ensures correct positioning of RNA polymerase II relative to the transcription start site, and (3) Disruption to the base pairing needed to form the open promoter complex is brought about by TFIIH. The final step in assembly of the initiation complex is the addition of phosphate groups to the C-terminal domain of the largest subunit of RNA polymerase II. Once phosphorylated, the polymerase is able to leave the PIC and begin synthesizing RNA.