23 CONTROLLING CHROMATIN STRUCTURE (Full Edition)
7 Acetylases are associated with activators
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Histone acetyltransferase (HAT) enzymes modify histones by addition of acetyl groups; some transcriptional coactivators have HAT activity.
- A deacetylase is an enzyme that removes acetyl groups from proteins.
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Histone deacetylases (HDAC) remove acetyl groups from histones; they may be associated with repressors of transcription.
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Deacetylated chromatin may have a more condensed structure.
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Transcription activators are associated with histone acetylase activities in large complexes.
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Histone acetylases vary in their target specificity.
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Acetylation could affect transcription in a quantitative or qualitative way.
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Acetylation is reversible. Each direction
of the reaction is catalyzed by a specific type of enzyme. Enzymes that
can acetylate histones are called histone acetyltransferases
or HATs; the acetyl groups are removed by histone
deacetylases or HDACs.
There are two groups of HAT enzymes: group A act on histones in
chromatin and are involved with the control of transcription; group B
act on newly synthesized histones in the cytosol, and are involved with
nucleosome assembly.
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Two inhibitors have been useful in
analyzing acetylation. Trichostatin and butyric acid inhibit histone
deacetylases, and cause acetylated nucleosomes to accumulate. The use
of these inhibitors has supported the general view that acetylation is
associated with gene expression; in fact, the ability of butyric acid
to cause changes in chromatin resembling those found upon gene
activation was one of the first indications of the connection between
acetylation and gene activity.
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The breakthrough in analyzing the role of
histone acetylation was provided by the characterization of the
acetylating and deacetylating enzymes, and their association with other
proteins that are involved in specific events of activation and
repression. A basic change in our view of histone acetylation was
caused by the discovery that HATs are not necessarily dedicated enzymes
associated with chromatin: rather it turns out that known activators of
transcription have HAT activity.
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The connection was established when the
catalytic subunit of a group A HAT was identified as a homologue of the
yeast regulator protein GCN5. Then it was shown that GCN5 itself has
HAT activity (with histones H3 and H4 as substrates). GCN5 is part of
an adaptor complex that is necessary for the interaction between
certain enhancers and their target promoters. Its HAT activity is
required for activation of the target gene (693).
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Figure 23.13
Coactivators may have HAT activities that acetylate the tails of nucleosomal histones.
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This enables us to redraw our picture for the action of coactivators as shown in Figure 23.13,
where RNA polymerase is bound at a hypersensitive site and coactivators
are acetylating histones on the nucleosomes in the vicinity (692).
Many examples are now known of interactions of this type.
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GCN5 leads us into one of the most
important acetylase complexes. In yeast, GCN5 is part of the 1.8 MDa
SAGA complex, which contains several proteins that are involved in
transcription (for review see 1969). Among these proteins are several
TAFIIs (696). Also, the TAFII145 subunit of TFIID
is an acetylase. There are some functional overlaps between TFIID and SAGA, most
notably that yeast can manage with either TAFII145
or GCN5, but is damaged by the deletion of both. This suggests that an
acetylase activity is essential for gene expression, but can be
provided by either TFIID or SAGA (1062). As might
be expected from the size of the SAGA complex, acetylation is only one
of its functions, although its other functions in gene activation are
less well characterized.
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One of the first general activators to be
characterized as an HAT was p300/CBP. (Actually, p300 and CBP are
different proteins, but they are so closely related that they are often
referred to as a single type of activity.) p300/CBP is a coactivator
that links an activator to the basal apparatus (see Figure 22.7).
p300/CBP interacts with various activators, including hormone
receptors, AP-1 (c-Jun and c-Fos), and MyoD. The interaction is
inhibited by the viral regulator proteins adenovirus E1A and SV40 T
antigen, which bind to p300/CBP to prevent the interaction with
transcription factors; this explains how these viral proteins inhibit
cellular transcription. (This inhibition is important for the ability
of the viral proteins to contribute to the tumorigenic state;
see Oncoproteins may regulate gene expression).
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p300/CBP acetylates the N-terminal tails
of H4 in nucleosomes. Another coactivator, called PCAF, preferentially
acetylates H3 in nucleosomes. p300/CBP and PCAF form a complex that
functions in transcriptional activation. In some cases yet another HAT
is involved: the coactivator ACTR, which functions with hormone
receptors, is itself an HAT that acts on H3 and H4, and also recruits
both p300/CBP and PCAF to form a coactivating complex. One explanation
for the presence of multiple HAT activities in a coactivating complex
is that each HAT has a different specificity, and that multiple
different acetylation events are required for activation.
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Figure 23.14
Complexes that modify chromatin structure or activity
have targeting subunits that determine their sites of action, HAT or
HDAC enzymes that acetylate or deacetylate histones, and effector
subunits that have other actions on chromatin or DNA.
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A general feature of acetylation is that a group A HAT is part of a large complex. Figure 23.14
shows a simplified model for their behavior. Typically the complex will
contain a targeting subunit(s) that determines the binding sites on
DNA. This determines the target for the HAT. The complex also contains
effector subunits that affect chromatin structure or act directly on
transcription. Probably at least some of the effectors require the
acetylation event in order to act. Deacetylation, catalyzed by an HDAC,
may work in a similar way.
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Acetylation occurs at both replication
(when it is transient) and at transcription (when it is maintained
while the gene is active). Is it playing the same role in each case?
One possibility is that the important effect is on nucleosome
structure. Acetylation may be necessary to "loosen" the nucleosome
core. At replication, acetylation of histones could be necessary to
allow them to be incorporated into new cores more easily. At
transcription, a similar effect could be necessary to allow a related
change in structure, possibly even to allow the histone core to be
displaced from DNA. Alternatively, acetylation could generate binding
sites for other proteins that are required for transcription. In either
case, deacetylation would reverse the effect.
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Is the effect of acetylation
quantitative or qualitative? One possibility is that a certain number
of acetyl groups are required to have an effect, and the exact
positions at which they occur are largely irrelevant. An alternative is
that individual acetylation events have specific effects. We might
interpret the existence of complexes containing multiple HAT activities
in either way — if individual enzymes have different specificities, we
may need multiple activities either to acetylate a sufficient number of
different positions or because the individual events are necessary for
different effects upon transcription. At replication, it appears, at
least with respect to histone H4, that acetylation at any two of three
available positions is adequate, favoring a quantitative model in this
case. Where chromatin structure is changed to affect transcription,
acetylation at specific positions is important (see Heterochromatin depends on interactions with histones).
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Last Revised on August 31, 2004
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692 Chen, H. et al. (1997). Nuclear
receptor coactivator ACTR is a novel histoneacetyltransferase and forms
a multimeric activation complex with P/CAF and CP/p300.
Cell 90, 569-580. PubMed Journal
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693 Brownell, J. E. et al.
(1996).
Tetrahymena histone acetyltransferase A: a homologue to yeast Gcn5p linking histone acetylation to gene activation.
Cell 84, 843-851.
PubMed Journal
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696 Grant, P. A. et al.
(1998).
A subset of TAFIIs are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation.
Cell 94, 45-53.
PubMed Journal
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1062 Lee, T. I., Causton, H. C., Holstege, F. C.,
Shen, W. C., Hannett, N., Jennings, E. G., Winston, F., Green, M. R.,
and Young, R. A. (2000). Redundant roles for the TFIID and SAGA
complexes in global transcription. Nature 405, 701-704.
PubMed Journal
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1969 Kingston, R. E. and Narlikar, G. J.
(1999).
ATP-dependent remodeling and acetylation as regulators of chromatin fluidity.
Genes Dev. 13, 2339-2352.
PubMed Journal
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©Jones and Bartlett Publishers (2007)
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