Eukaryotic RNA Polymerases
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.
- RNA polymerase I is responsible for transcribing RNA that codes for genes
that become structural components of the ribosome, a protein responsible for the
translation of RNA into proteins.
- RNA polymerase II transcribes protein-encoding genes, or messenger RNAs,
which are the RNAs that get translated into proteins.
- RNA polymerase III transcribes a different structural region of the
ribosome, transfer RNAs, which are also involved the translation process, as
well as non-protein encoding RNAs.
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.
Transcription Machinery
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.
