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Promoters and Enhancers
Chapter 24
24.1 Introduction
Figure 24.1
2
24.2 Eukaryotic RNA Polymerases Consist
of Many Subunits
• RNA polymerase I synthesizes rRNA in the
nucleolus.
• RNA polymerase II synthesizes mRNA in
the nucleoplasm.
• RNA polymerase III synthesizes small
RNAs in the nucleoplasm.
3
• All eukaryotic RNA polymerases have ∼12 subunits and are
aggregates of >500 kD.
• Some subunits are common to all three RNA polymerases.
• The largest subunit in RNA polymerase II has a CTD (carboxyterminal domain) consisting of multiple repeats of a heptamer.
4
Figure 24.2
24.3 Promoter Elements Are Defined by
Mutations and Footprinting
• Promoters are defined by their ability to cause
transcription of an attached sequence in an
appropriate test system in vitro or in vivo.
5
Figure 24.3
24.4 RNA Polymerase I Has a Bipartite
Promoter
• The RNA polymerase I promoter consists of:
– a core promoter
– an upstream control element (UPE)
6
Figure 24.5
• The factor UBF1 wraps DNA around a protein
structure to bring the core and UPE into
proximity.
• SL1 includes the factor TBP that is involved in
initiation by all three RNA polymerases.
• RNA polymerase binds to the UBF1-SL1
complex at the core promoter.
7
24.5 RNA Polymerase III Uses Both
Downstream and Upstream Promoters
• RNA polymerase III has two types of promoters.
8
Figure 24.7
• Internal promoters:
– have short consensus
sequences located within
the transcription unit
– cause initiation to occur a
fixed distance upstream
Figure 24.6
• Upstream promoters
contain three short
consensus sequences
upstream of the startpoint
that are bound by
transcription factors.
9
24.6 TFIIIB Is the Commitment Factor for Pol
III Promoters
• TFIIIA and TFIIIC bind to the
consensus sequences and
enable TFIIIB to bind at the
startpoint.
• TFIIIB has TBP as one subunit
and enables RNA polymerase
to bind.
10
Figure 24.9
24.7 The Startpoint for RNA Polymerase II
• RNA polymerase II requires general
transcription factors (called TFIIX) to
initiate transcription.
• RNA polymerase II promoters have a short
conserved sequence Py2CAPy5 (the
initiator InR) at the startpoint.
11
• The TATA box is a common component of RNA polymerase II promoters
– It consists of an A-T-rich octamer located ~25 bp upstream of the startpoint.
• The DPE is a common component of RNA polymerase II promoters that do
not contain a TATA box.
• A core promoter for RNA polymerase II includes:
– the InR
– either a TATA box or a DPE
Figure 24.10
12
24.8 TBP Is a Universal Factor
• TBP is a component of the
positioning factor that is required
for each type of RNA polymerase
to bind its promoter.
• The factor for RNA polymerase II is
TFIID, which consists of:
• TBP
• 11 TAFs
– The total mass is ∼800 kD.
13
Figure 24.11
24.9 TBP Binds DNA in an Unusual Way
• TBP binds to the TATA box in the minor
groove of DNA.
• It forms a saddle around the DNA and
bends it by в€ј80В°.
• Some of the TAFs resemble histones and
may form a structure resembling a histone
octamer.
14
24.10 The Basal Apparatus Assembles at
the Promoter
• Binding of TFIID to the TATA box
is the first step in initiation.
• Other transcription factors bind
to the complex in a defined order
– This extends the length of the
protected region on DNA.
• When RNA polymerase II binds
to the complex, it initiates
transcription.
15
Figure 24.14
24.11 Initiation Is Followed by Promoter
Clearance
• TFIIE and TFIIH are required to
melt DNA to allow polymerase
movement.
• Phosphorylation of the CTD may
be required for elongationto
begin.
• Further phosphorylation of the
CTD is required at some
promoters to end abortive
initiation.
16
Figure 24.17
• The CTD may coordinate
processing of RNA with
transcription.
17
Figure 24.18
24.12 A Connection between Transcription
and Repair
• Transcribed genes are
preferentially repaired when DNA
damage occurs.
18
Figure 24.19
• TFIIH provides the
link to a complex of
repair enzymes.
• Mutations in the XPD
component of TFIIH
cause three types of
human diseases
19
Figure 24.20
24.13 Short Sequence Elements Bind
Activators
• Short conserved sequence elements are
dispersed in the region preceding the
startpoint.
• The upstream elements increase the frequency
of initiation.
• The factors that bind to them to stimulate
transcription are called activators.
20
24.14 Promoter Construction Is Flexible but
Context Can Be Important
• No individual upstream
element is essential for
promoter function;
– Although one or more elements
must be present for efficient
initiation.
• Some elements are
recognized by multiple
factors.
Figure 24.22
– The factor that is used at any
particular promoter may be
determined by the context of the
other factors that are bound.
21
24.15 Enhancers Contain Bidirectional
Elements That Assist Initiation
• An enhancer activates the nearest promoter to
it.
– It can be any distance either upstream or
downstream of the promoter.
22
Figure 24.23
• A UAS (upstream activator sequence) in yeast
behaves like an enhancer but works only
upstream of the promoter.
• Similar sequence elements are found in
enhancers and promoters.
• Enhancers form complexes of activators that
interact directly or indirectly with the promoter.
23
24.16 Enhancers Contain the Same
Elements That Are Found at Promoters
• Enhancers are made of the same short sequence elements
that are found in promoters.
• The density of sequence components is greater in the
enhancer than in the promoter.
24
Figure 24.24
24.17 Enhancers Work by Increasing the
Concentration of Activators Near the Promoter
• Enhancers usually work only in cis
configuration with a target promoter.
• Enhancers can be made to work in trans
configuration by:
– linking the DNA that contains the target
promoter to the DNA that contains the
enhancer via a protein bridge or
– catenating the two molecules
25
• The principle is that an enhancer works in any
situation in which it is constrained to be in the
same proximity as the promoter.
26
Figure 24.25
24.18 Gene Expression Is Associated with
Demethylation
• Demethylation at the 5′ end of the gene is
necessary for transcription.
27
24.19 CpG Islands Are Regulatory Targets
• CpG islands surround the promoters of
constitutively expressed genes where they
are unmethylated.
• CpG islands also are found at the
promoters of some tissue-regulated
genes.
28
• There are ∼29,000 CpG islands in the
human genome.
• Methylation of a CpG island prevents
activation of a promoter within it.
• Repression is caused by proteins that bind
to methylated CpG doublets.
29
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