EUKARYOTIC TRANSCRIPTION

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 PROKARYOTIC VERSUS EUKARYOTIC TRANSCRIPTION

• Bacteria have only one RNA polymerase whereas all eukaryotes have at least three
different ones (Pol I, II, and III); plants also have a Pol IV and a Pol V

• Bacteria require only one additional initiation factor (σ), several initiation factors
are required for efficient and promoter-specific initiation in eukaryotes. These are
called the general transcription factors (GTFs).
RNA Polymerase II Core Promoters are made up of combinations of different classes of
Sequence Element
• The eukaryotic core promoter refers to the minimal set of
sequence elements required for accurate transcription
initiation by the Pol II machinery, as measured in vitro

• A core promoter is typically 40–60 nucleotides long, extending

either upstream or downstream from the transcription start
site.
RNA Polymerase II forms a preinitiation complex with general Transcription Factors
at the Promoter
• The complete set of general
transcription factors and RNA
polymerase, bound together at
the promoter and poised for
initiation, is called the
preinitiation complex.
• “TFII” denotes a transcription
factor for Pol II, with individual
factors distinguished as A, B,
and so on
• The component of TFIID that
binds to the TATA DNA
sequence is called TBP (TATA-
binding protein). The other
subunits in this complex are
called TAFs, for TBP-
associated factors.
In contrast to the situation in bacteria, promoter melting (formation of
open complex) in eukaryotes requires hydrolysis of ATP and is mediated
by TFIIH.
• There is a period of abortive initiation before the polymerase escapes the
promoter and enters into the elongation phase
• Abortive initiation in prokaryotes: RNA polymerase synthesizes a series of
short transcripts

• Promoter escape in eukaryotes:

1) ATP hydrolysis (in addition to the earlier ATP hydrolysis needed for DNA
melting)
2) Phosphorylation of the polymerase
PHOSPHORYLATION OF THE POLYMERASE OCCURS AT CTD
In Vivo, Transcription Initiation Requires Additional Proteins, Including the Mediator Complex
• One reason for additional requirements is that the DNA template in vivo is
packaged into chromatin. This condition complicates binding to the promoter of
polymerase and its associated factors
• Transcriptional regulatory proteins called activators help recruit polymerase to
the promoter, stabilizing its binding there. This recruitment is mediated
through interactions between DNA-bound activators, chromatin-modifying and
-remodeling factors, and parts of the transcription machinery
• One such interaction is with the Mediator complex. Mediator is associated with
the basic transcription machinery, most likely touching the CTD “tail” of the
large polymerase subunit through one surface, while presenting other surfaces
for interaction with DNA-bound activators.
Mediator Consists of Many Subunits, Some Conserved from Yeast to Human
A New Set of Factors Stimulates Pol II Elongation and RNA Proofreading
 POST TRANSCRIPTIONAL PROCESSING OF EUKARYOTIC RNA

Once transcribed, eukaryotic RNA has to be processed in various ways before

being exported from the nucleus where it can be translated. These processing
events include:
1)Capping of the 5’ end of the RNA
2) Splicing (the process whereby non-coding introns are removed from RNA to
generate the mature mRNA.)
3) Polyadenylation of the 3’ end of the RNA
The structure and formation of the 5’ RNA cap

The resulting 5’ cap structure

subsequently recruits the ribosome
to the mRNA for translation to
begin
Polyadenylation and termination

Two protein complexes are carried by the CTD of

polymerase as it approaches the end of the gene:
1) CPSF (cleavage and polyadenylation specificity
factor) 2) CSTF (cleavage stimulation factor)

The long tail of As is unique to transcripts made by Pol

II