Transcription is more complicated process in eukaryotes compare to prokaryotes. In eukaryotes, three different RNA polymerases transcribe the genes for the four types of RNAs.
RNA Polymerase I: It is located in the nucleolus. RNA polymerase I enzyme transcribes genes encoding three of the four ribosomal RNAs (18S, 28S and 5.8S). It is responsible for the synthesis of precursors for the large ribosomal RNAs.
RNA Polymerase II: It is found in the nucleoplasm of the nucleus. The main function of this enzyme is synthesis of messenger RNAs (MRNAs) and some small nuclear RNA. (snRNAs). RNA polymerase II can recognize thousands of promoters that vary greatly in sequence.
RNA Polymerase III: It is located in the nucleoplasm. It synthesizes the transfer RNAs (tRNAs), 5S rRNAs and some other small specialised RNAs.
RNA polymerase II is central to eukaryotic gene expression and a huge enzyme with 12 subunits. The process of transcription by Pol II can be classified in the form of phases such as assembly, initiation, elongation and termination.
The core promoter is needed for the transcription machinery to start RNA synthesis at the correct site. The core promoter elements are Inr (initiator) and TATA box (Goldberg -Hogness box). Initiator spans the transcription initiation start site (+1) while the TATA element located at -30 position, Promoters contain various combinations of core promoter elements and promoter proximal elements. Enhancers are also required for the maximal transcription of a gene. It contains a variety of short sequence elements. Activators mainly bind to these elements and with other protein complexes.
RNA polymerase II and general transcription factors (GTFs) are mainly responsible for initiation of transcription. All three eukaryotic RNA polymerases require GTFS in order to initiate transcription. RNA polymerase is attached to the TATA box with the help of a series of transcription factors specific to RNA polymerase II (TFⅡA, TFⅡB etc). These bind to the DNA around the TATA box and form a platform for binding RNA polymerase II. Transcription factors can bind in a specific order as TFⅡD binds first followed by TFⅡA and TFⅡB. The RNA polymerase I then binds followed by TFⅡF, E, H and J to produce a functional complex capable of initiating transcription (Fig. 8.12). TFⅡH has DNA helicase activity that promotes the unwinding of DNA near the RNA start site and it creates a open complex. TFⅡE and TFⅡH are released during synthesis of initial 60 to 70 nucleotides of RNA. RNA polymerase II enters in the elongation phase of transcription. Elongation is accompanied by the release of many transcription factors and is enhanced by elongation factors. Transcription is terminated when the RNA transcript is completed. Pol Ⅱ is dephosphorylated and recycled.