Unlike prokaryotic RNA polymerase that initiates the transcription of all different types of RNA, RNA polymerase in eukaryotes (including humans) comes in three variations, each encoding a different type of gene.
The promoter regions for RNA polymerases I and II are located upstream of the start site, but the promoter for polymerase III is oddly located downstream.
One key difference between prokaryotic and eukaryotic transcription is that eukaryotic polymerases are unable to recognize promoter regions. They have no direct parallel to the sigma subunit of their prokaryotic counterpart. Instead, eukaryotic polymerases depend on other proteins that bind to the promoter regions and then recruit the RNA polymerases to the correct spots.
Unlike prokaryotic promoters, eukaryotic promoter regions do not have a "canonical sequence". They do, however, have more flexible modular elements. The polymerase II promoter, for example, has a number of traditional sequences that can appear either in tandem or alone. At the least, polymerase II promoters must have either a "TATA box", a region approximately 25 base pairs upstream from the start-site with the sequence TATAAAA, or an "initiator element". The TATA box, loosely resembles the -10 region found in prokaryotic promoters, but the initiator element is not as well defined. It is known to straddle the start-site.
Other non-universal sequences include the "CAAT box" (GGCCAATCT) and the "GC box" (GGGCG). Each of these sequences act as binding sites for specific transcription factors that then recruit the appropriate RNA polymerases. The most important polymerase II transcription factor is the TATA-binding protein, which binds to the TATA box promoter, where it sits on the DNA and makes contact with its minor groove. This factor is universally involved in polymerase II promoter recognition.
The eukaryotic transcription machinery is complex. It is a compact structure of different proteins that are bound at different positions on a DNA strand. Because the eukaryotic DNA template is bound in nucleosomes, it is not completely exposed, as is prokaryotic DNA. As a result, eukaryotic transcription machinery must be able to penetrate chromatin layers in order to contact the DNA. The activity of the transcription machinery can be influenced by proteins that are bound to specific promoters.
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