Function of RNA Polymerase II

The position of the general transcription factors with respect to promoter DNA in the initiation complex can be inferred from site-specific protein-DNA crosslinking (Ebright, 1998). The crosslinking data, taken 

After loading of promoter DNA onto Pol II, duplex DNA is melted upstream of the transcription start site (Holstege et al., 1997 Pan and Greenblatt, 1994 Wang et al., 1992). DNA melting requires TFIIH, which 

Transitions that underlie promoter clearance may be rationalized with the Pol II structures. At the very beginning of transcription, contacts of Pol II with nascent RNA are crucial. To allow for the synthesis of the first phosphodiester bond, nucleoside triphosphates must be held by the protein. The resulting dinucleotide RNA must still be held by protein— RNA contacts, as observed in the core elongation complex structure (Gnatt et al., 2001), as the energy of base-pairing alone is insufficient for its retention. Equally, RNA is still bound by Pol II at the position of the third nucleotide. Despite the observed RNA-Pol II contacts, short RNA 

After successful promoter clearance, the early elongation complex can pause in a promoter proximal position (Albert et al., 1997 Li et al., 1996 Raschke et al., 1999). This promoter-proximal pausing of polymerase 

A functional model of the elongation complex was derived for bacterial RNA polymerase from biochemical data (Korzheva et al., 1998 Nudler, 1999). X-ray crystallographic data and site-specific protein-nucleic acid 

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RNA polymerase I (Pol I) is responsible for the synthesis of only one type of RNA, a transcript called pre-ribosomal RNA (or pre-rRNA), which contains the precursor for the 18S, 5.8S, and 28S rRNAs (see Fig. 26-22). Pol I promoters vary greatly in sequence from one species to another. The principal function of RNA polymerase II (Pol II) is synthesis of mRNAs and some specialized RNAs. This enzyme can recognize thousands of promoters that vary greatly in sequence. Many Pol II promoters have a few sequence features in common, including a TATA box (eukaryotic consensus sequence TATAAA) near base pair —30 and an Inr sequence (initiator) near the RNA start site at +1 (Fig. 26-8). 

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