Latchman. Eukariotic Transciption Factors
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REPRESSION OF GENE EXPRESSION BY TRANSCRIPTION FACTORS 201
Figure 6.22
Binding of TFIIA to TBP
prevents inhibitory
molecules (I) from
binding but still allows
the binding of TFIIB and
thereby promotes the
assembly of the basal
transcriptional complex.
Figure 6.23
A repressor of
transcription (R) can act
by inducing a tightly
packed chromatin
structure incompatible
with transcription.
directing the tight packing of specific genes and thereby pr eventing transcrip-
tion, the polycomb factor evidently has the opposite effect to that of the
GAGA/trithorax factor which, as discussed in section 5.5.1, directs an open
chromatin structure allow ing activator binding (Fig. 6.24) (for reviews see
Schumacher and Magnus son, 1997; Simon and Tamkun, 2002).
Interestingly, both the polycomb and trithor ax factors have been shown to
affect the function of insulator elements (see Chapter 1, section 1.3.5) with
mutation of polycomb preventing the blocking effects of insulators on enhan-
cer function, while mutation of trithorax enhances the blocking effects of
insulators. Hence, insulator elements represent one target for the antagonistic
effects of polycomb and trithorax factors (Gerasimova and Corces, 1998).
It has recently been shown that the polycomb factor forms part of a multi-
protein complex that has histone methyltransferase activity (Czermin et al.,
2002; Mu
¨
ller et al., 2002). As discussed in Chapter 1 (section 1.2.3) the methy-
lation of histones can produce a tightly packed chromatin structure and hence
this is one mechanism by which polycomb can produce a closed chromatin
structure.
As well as targeting histones at the level of methylation, transcriptional co-
repressors such as the NuRD and SIN3 complexes can also produce a more
tightly packed chromatin structure by acting as histone deacetylases, removing
the acetyl groups which promote chromatin opening (for reviews see
Ahringer, 2000; Ng and Bird, 2000) (see Chapter 1, section 1.2.3). This effect
evidently parallels the ability of transcriptional co-activators to produce a
more open chromatin structure by acetylating histones (see Chapter 5, section
5.5.1).
202 EUKARYOTIC TRANSCRIPTION FACTORS
Figure 6.24
The GAGA/trithorax
factor induces an open
chromatin structure. Its
inactivation by mutation
produces an
inappropriate tightly
packed chromatin
structure of its target
genes producing a failure
of gene transcription. In
contrast, the polycomb
factor (PC) induces a
tightly packed chromatin
structure. Its inactivation
by mutation produces
inappropriate chromatin
opening and
transcription.
Hence the state of his tone acetylation and the structure of chromatin can
be controlled by the balance of deacetylases and acetylases which are bound to
the DNA (Fig. 6.25). In most cases the acetylating and deacetylating factors
will be respectively co-activators and co-repressors and will be brought to the
DNA via interactions with distinct activating and inhibiting transcription fac-
tors respectively. In the case of the thyroid hormone receptor, however, both
types of factors bind to the same molecule. Thus, the N-CoR co-repressor,
which binds to the thyroid hormone receptor prior to exposure to hormone,
also binds other co-repressor complexes such as mRPD3 and SIN3 which have
histone deacetylase activity. Conversely, following hormone binding, these
factors dissociate and are replaced by co-activators such as CBP which acety-
late histones and allow the receptor to activate transcription (Fig. 6.26).
Hence, transcriptional repressors can modu late chromatin structure, acting
at least in part by altering the histone code enhancing methylation and
reducing acetylation.
REPRESSION OF GENE EXPRESSION BY TRANSCRIPTION FACTORS 203
Figure 6.26
The inhibitory domain
(hatched semi-circle) of
the thyroid hormone
receptor binds a co-
repressor (Co-R) complex
which deacetylates
histones inducing a closed
chromatin structure (wavy
line). Binding of ligand
results in the release of
the co-repressor and
binding of co-activator
(Co-A) molecules to the
exposed activation domain
(solid square). The co-
activators have histone
acetyltransferase activity
and produce a more open
chromatin structure (solid
line) compatible with
transcription.
Figure 6.25
The balance between
tightly packed chromatin
(wavy line) and open
chromatin (solid line) can
be controlled by the
balance between co-
activating molecules which
acetylate histones and co-
repressors which
deacetylate histones in
the nucleosome (N).
6.4.2 INHIBITION OF T RANSCRIPTION ELONGATION
Just as activators can stimulate transcriptional elongation, as well as transcrip-
tional initiation (see Chapter 5, section 5.5.2) repressors can inhibit transcrip-
tion by blocking transcriptional elongation. Thus, the zebrafish Foggy protein
acts by interacting with the non-phosphorylated form of RNA polymerase and
prevents it from catalysing transcriptional elongation. When the polymerase is
phosphorylated on its C-terminal domain (see Chapter 3, section 3.5.1), it is
no longer inhibited by Foggy and transcriptional elongation proceeds (Guo et
al., 2000) (Fig. 6.27). Importantly, when Foggy is mutated so that it cannot
block transcriptional elongation, the development of the zebrafish nervous
system is severely disrupted. This indicates that the correct regulat ion of
transcriptional elongation by proteins such as Foggy is necessary for normal
development.
Inhibition of tr anscriptional elongation is also produced by the von
Hippel–Lindau protein (VHL). However, this factor targets the phosphory-
lated form of RNA polymerase. Thus, VHL forms part of a complex which
adds the small protein ubiquitin to the large subunit of RNA polymerase II
(see Chapter 8, section 8.4.5 for further details of this protein modification).
This ubiquitination occurs only for the phosphorylated form of RNA poly-
merase II and targets it for degradation, thereby blocking transcriptional
elongation (Kuznetsova et al., 2003), (Figure 6.28). As with Foggy, the action
of VHL is of critical importance for normal cell function. Thus, as discussed in
Chapter 9 (section 9.4.4), VHL is an anti-oncogene and cancer s result when
the functio n of VHL is disrupted by mutations.
204 EUKARYOTIC TRANSCRIPTION FACTORS
Figure 6.27
Phosphorylation of the C-
terminal domain (CTD) of
RNA polymerase prevents
binding of the Foggy
protein which would
otherwise inhibit
transcriptional elongation.
Hence, transcriptional elongation can be repressed both by Foggy which
inhibits the non-phosphorylated form of RNA polymerase II and by VHL
which targets the phosphorylated form of the polymerase for degradation.
As with transcript ional initiation, the correct regulation of these inhibitory
processes and their activity relative to processes which stimulate transcrip-
tional elongation (see Chapter 5, section 5.5.2) is likely to be critical for the
correct regulation of cellular function.
6.5 CONCLUSIONS
In this chapter, we have discussed how the repression of transcription can be
produced by the neutralization of a positively acting factor, or by direct
repression of the basal transcriptional complex as well as by alteration of
chromatin structure or the inhibition of transcriptional elongation. These
properties offer ample scope for gene regulation in different cell types or
in different tissues. Thus in addition to the simple activation of gen e expres-
sion by a positively acting factor present in only one cell type, the effect of a
positively acting factor present in several different cell types can be affected by
the presence or absence of a negatively acting factor which is active in only
one cell type and which inhibits its activity. Similarly, a single factor may act
either positively or negatively depending on the gene involved (as in the case
of the glucocorticoid receptor) or depending on whether a specific hormone
is present (as in the case of the thyroid hormone receptor).
Interestingly, two positive factors can also repress one another if they com-
pete for the same co-factor. Thus, glucocorticoid hormones have been known
for some time to be a potent inhibitor of the induction of the collagenase
gene by phorbol esters resulting in their having an anti-inflammatory effect.
This inhibition is mediated by the glucocorticoid receptor which inhibits the
activity of the Jun and Fos proteins that normally activate the collagenase gene
via the AP-1 sites in its promoter (for discussion of Fos, Jun and AP-1 see
REPRESSION OF GENE EXPRESSION BY TRANSCRIPTION FACTORS 205
Figure 6.28
The von Hippel-Lindau
gene product (VHL) adds
ubiquitin (Ubi) to the
phosphorylated C-terminal
domain (CTD) of RNA
polymerase. This
promotes degradation of
the polymerase inhibiting
transcriptional elongation.
Chapter 9, section 9.3.1). This effectively inhibits collagenase gene activation.
Unlike the examples of repression by the glucocorticoid receptor discussed in
section 6.2.1, however, the collagenase promoter does not con tain any bind-
ing sites for the receptor adjacent to the AP-1 sites, nor does the receptor
apparently bind to the collagenase promoter.
Interestingly, however, like the glucocorticoid receptor, the Fos/Jun com-
plex requires the CBP protein as a co-activator to acti vate transcription.
Hence, the glucocorticoid receptor may compete with Fos/Jun for limited
quantities of the CBP co-activator which are present in the cell resulting in
a failure of Fos/Jun to activate in the presence of activated glucocorticoid
receptor (Kamei et al., 1996) (Fig. 6.29). Clearly, such competition between
Fos/Jun and the glucocorticoid receptor for limited quantities of CBP will
also result in inhibition of glucocorticoid-dependent gen es in response to
hormone in the presence of high concentrations of Fos and Jun and this is
indeed observed (Fig. 6.29).
Hence, mutual transrepression of two different activating proteins can be
achieved by competition for a co-activator (Fig. 6.29). Moreover, this mutual
repression illustrates how different cellul ar signalling pathways, which are
activated respectively by phorbol esters and glucocorticoid hormones, can
interact with one another resulting in cross talk between the pathways (for
review see Janknecht and Hunter, 1996).
Hence, as well as being able to activate gene expression, the members of
the steroid/thyroid hormone receptor family also illustrate three mechanisms
by which repression of gene expression can be achieved namely, the direct
inhibition of transcription (see section 6.3.2), the neutralization of a positive
206 EUKARYOTIC TRANSCRIPTION FACTORS
Figure 6.29
Mutual transrepression by
Fos/Jun and the
glucocorticoid receptor.
Competition between
Fos/Jun and the
glucocorticoid receptor for
the CBP co-activator
inhibits the expression of
genes containing binding
sites for either Fos/Jun
(AP-1 sites) or for the
glucocorticoid receptor
(GRE).
factor either by preventing its binding to DNA by masking of its site (see
section 6.2.1), or by competing for a co-activator (see above). It should be
noted, however, that these three examples differ in that the glucocorticoid
receptor needs to be activated by steroid before it can inhibit gene expression
by binding to an nGRE or competing for CBP whereas the thyroid hormone
receptor directly inhibits by binding to its res ponse element in the absence of
hormone.
Hence, numerous methods of transcriptional repression exist paralleling
the different mechanisms of transcriptional activation discussed in Chapter 5.
Ultimately, however, as with transcriptional activation, all such potential
mechanisms involving the inhibition of gene expression in response to spe-
cific stimuli or in specific cell types are dependent upon mechanisms that
control the synthesis or activity of specific transcription factors in different
cell types or in response to specific stimuli. These mechanisms are discussed
in the next two chapters.
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