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Combinatorial gene regulation by eukaryotic transcription factors
Lin Chen
Recent structure determinations of high order complexes of
eukaryotic transcription factors bound to DNA have revealed
that residues from their DNA-binding domains are involved in
protein–protein interactions between distinct factors.
Protein–protein interactions between transactivation domains
and coactivators have also been characterized in a number of
recently determined structures. These studies support the
combinatorial mechanism of transcription regulation in
eukaryotic cells and multicellular organisms.
Addresses
Department of Chemistry and Biochemistry, University of Colorado at
Boulder, Boulder, CO 80309-0215, USA;
e-mail: [email protected]
Figure 1
(a)
MCM1 MADS box dimer
C
C
N
Flexible linker
β hairpin
C
C
Modeled half-site
N
MATα2 homeodomain
N
Current Opinion in Structural Biology 1999, 9:48–55
http://biomednet.com/elecref/0959440X00900048
N
(b)
Flexible linker
© Elsevier Science Ltd ISSN 0959-440X
Abbreviations
AF-2
activation function-2
AP-1
activating protein-1
CBP
CREB-binding protein
CRE
cAMP-response element
CREB CRE-binding protein
GABP GA-binding protein
GTF
general transcription factor
IFN
interferon
IL
interleukin
KIX
CREB-binding domain of CBP
LBD
ligand-binding domain
NFAT
nuclear factor of activated T cells
κB nuclear factor κB
NF-κ
pKID
phosphorylated kinase-inducible domain
PPAR-γγ peroxisome proliferator-activated receptor-γ
RHR
Rel homology region
SRC
steroid receptor coactivator
STAT
signal transducer and activator of transcription
TAF
TBP-associated factor
TBP
TATA-box-binding protein
TCR
T-cell receptor
TF
transcription factor
VP-16 herpes simplex virus protein-16
Introduction
Regulated eukaryotic gene transcription involves the
assembly of an initiation complex at the core promoter
region and regulatory complexes at promoterenhancer/operator regions [1]. The core promoter complex
of RNA polymerase II contains multiple protein factors
(referred to as general transcription factors, GTFs), including the TATA-box-binding protein (TBP) and its
associated factors (TAFs). The structures of a number of
binary and ternary GTF–DNA complexes have been
determined in previous years [2–4]. More GTF complexes
will probably appear soon. Structural studies of eukaryotic
transcription factors continue to reveal novel DNA-binding motifs and variants of known motifs [5•,6•,7,8•]. Many
of these studies from the past year will not be discussed
'Arm'
β hairpin
MATα2
homeodomain
MCM1
MADS box dimer
Modeled half-site
Current Opinion in Structural Biology
The structure of MCM1 (residues 1–100) and MATα2 (residues
103–189) bound to DNA. On a natural a-specific operator, the MCM1
MADS box DNA-binding site is flanked on both sides by a MATα2 site.
The MADS box dimer and the left hand MATα2 homeodomain bound
to DNA is the crystallographically observed complex [9••]. The
MATα2–DNA complex on the right hand (light shading and thin stick
DNA drawing) was modeled manually to represent a
MATα2–MCM1–MATα2 complex on an a-specific operator. Each
subunit is shaded differently. Note that the β hairpin of MATα2 extends
the central β sheet of MCM1, which forms the major protein–protein
interaction interface. The β-strand interaction is probably conserved in
the modeled right-hand half-site, but the rest of the linker and the DNA
conformation may be different with different DNA spacing. (a) View
perpendicular to the MCM1 dimer dyad axis. (b) View from the top,
with a rotation 90° from (a). Note the conserved minor groove DNA
binding by the MATα2 homeodomain ‘arm’. All figures drawn using
MOLSCRIPT [52].
here because of the limited space. This review will focus
on recent structural studies of high order regulatory complexes [9••–11••] and activation domain–coactivator
complexes [12••–15••].
The activation of eukaryotic genes in vivo often requires
the coordinated binding of multiple transcription factors
to the promoter-enhancer region; many of these factors
are regulated by distinct signal transduction pathways. In
several cases, it has been shown that the binding of multiple transcription factors to a specific promoter-enhancer
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Combinatorial gene regulation by eukaryotic transcription factors Chen
region is cooperative and requires a unique composition
and spatial arrangement of transcription-factor-binding
sites [16•,17,18]. The assembly of these enhancer complexes (also referred to as the enhanceosome [19]) is
facilitated by protein–protein interactions between
DNA-bound factors and protein-induced DNA bending.
Two features of enhanceosome assembly are especially
important for combinatorial transcription regulation: combinations of multiple transcription factors generate
diverse patterns of regulation [20,21] and highly cooperative binding ensures the specificity of transcriptional
control [22].
The enhanceosome may serve as a template for the
assembly of the core promoter complex by either direct or
coactivator-mediated interactions. Most eukaryotic transcription factors contain one or more transactivation
domain involved in interactions with downstream coactivators and GTFs [23]. These transactivation domains are
usually rich in proline and glutamine, or acidic amino
acids, and appear to be very flexible before binding to
their respective targets. This flexibility is probably the
main reason that the structural characterization of these
domains lagged behind that of the DNA-binding
domains. The recent identification of various targets of
transactivation domains, including TAFs, cAMPresponse element (CRE) binding protein (CREB)
binding proteins (CBPs/p300) and steroid receptor coactivators (SRCs), however, has allowed the structural
characterization of several transactivation domains in
complex with their respective target proteins [12••–15••].
Structures of eukaryotic transcription factor
complexes bound to DNA
In Saccharomyces cerevisiae, three transcription factors, the
homeodomain proteins MATα2 and MATaa1, and the
MADS box protein MCM1, play crucial roles in cell-type
specification. Various combinations of these three factors
and additional factors are involved in gene activation and
repression in different yeast cell types, providing the best
example of the combinatorial control of eukaryotic gene
regulation [24]. These transcription factors bind various
DNA sites cooperatively to form higher order complexes
that have distinct regulatory functions. The crystal structure of a MATα2–MATaa1–DNA ternary complex revealed
that cooperative DNA binding is induced by a C-terminal
amphipathic α helix of MATα2 bound to a hydrophobic
groove on the MATaa1 homeodomain [25]. In another complex, that of MATα2–MCM1–MATα2–DNA, an
N-terminal flexible linker of MATα2 has been suggested
by biochemical studies to interact with the DNA-binding
domain (referred to as the MADS box) of MCM1 to mediate cooperative DNA binding [26]. Indeed, the recent
crystal structure of a DNA-bound ternary complex of
MCM1 and MATα2 [9••] shows that part of this flexible
linker forms a β hairpin that binds to the outer strand of the
central β sheet of the MCM1 MADS box (Figure 1). The
binding interactions involve parallel β-strand hydrogen
49
Figure 2
Jun
Fos
NFAT1
RHR-N
Loop 1
NFAT1
RHR-C
Loop 2
Loop 3
DNA
Current Opinion in Structural Biology
The structure of NFAT1 (residues 399–678), Fos (residues 138–200)
and Jun (residues 254–315) bound to DNA [10••]. Multiple loops (loops
1, 2 and 3 are shown in this orientation) presented by the NFAT Nterminal RHR (RHR-N) contact Fos and Jun. Each component (Fos, Jun
and the two NFAT domains [RHR-N and RHR-C]) is shaded differently.
bonding of mainchain atoms and hydrophobic packing of
sidechains. β-strand-mediated interactions have also been
observed between TFIIA and TBP in TFIIA–TBP–DNA
complexes [3,4] and may be involved in a wide range of
physiological and pathological protein–protein interactions.
Combinatorial control of transcription activation in higher eukaryotic cells has been characterized biochemically
for several promoter-enhancers, including that of the
TCR α gene [18], the IFN-β gene [16•] and the interleukin (IL)-2 gene [27]. A crystallographic study of this
last was reported recently [10••]. The nuclear factor of
activated T cells (NFAT) and members of the activating
protein-1 (AP-1) transcription factor family (including
Fos and Jun) bind cooperatively to their target DNA sites
in the promoter-enhancer and participate in the transcriptional regulation of IL-2 and other immune response
genes [28]. Although NFAT is activated by calcium signals through calcineurin, the AP-1 transcription factors
are induced by agents that activate protein kinase C. The
DNA-binding domain of NFAT is distantly related to
that of the Rel family of transcription factors, including
the nuclear factor-KB (NF-KB) proteins. The DNA-binding domains of AP-1 proteins consist of the basic region,
leucine zipper (bZIP) motif. The DNA-binding domains
of NFAT, Fos and Jun are necessary and sufficient for
cooperative DNA binding. The recently determined
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Protein–nucleic acid interactions
enhances GABPα DNA binding both by displacing the
C-terminal α helix from its inhibitory orientation and by
directly stabilizing the DNA-binding residues of
GABPα. GABPβ is also thought to mediate the higher
order assembly of a GABPβ/α complex on DNA (αβ–αβ
dimer) through its C-terminal leucine zipper motif.
Figure 3
GABPβ
GABPα
Ankyrin repeats
C-terminal
helix
Ets domain
DNA
Current Opinion in Structural Biology
Complex of GABPβ (residues 1–157) and GABPα (residues
311–430) bound to DNA [11••]. Each subunit is shaded differently
(GABPβ dark and GABPα light). Note that the GABPβ ankyrin repeats
bind to the GABPα Ets domain and the C-terminal α helix using the
extended loop tips. The ankyrin repeats of GABPβ do not contact the
DNA in this structure.
crystal structure of this complex [10••] shows
protein–protein interactions between NFAT and Fos–Jun
that involve multiple patches of surface residues on the
three proteins and that are facilitated by the bending of
the DNA and the Fos α helix (Figure 2). Previous biochemical studies had suggested that many of these
interacting residues were important for complex assembly [29–31]. In the ternary complex, the NFAT
DNA-binding domain seems to have moved closer to
Fos–Jun from its orientation in the binary NFAT–DNA
complex [32•]. The interaction surfaces are mostly
hydrophilic, with a small hydrophobic center.
DNA binding by a transcription factor can also be modulated by interactions with a protein that does not bind
DNA itself. One example is the GA-binding protein
(GABP) that binds DNA with a conserved GA sequence
motif, whose core DNA-binding complex structure was
recently determined [11••] (Figure 3). The two subunit
GABP complex is involved in the transcriptional regulation of mitochondrial protein genes and some viral
genes. GABPα belongs to the Ets family of transcription
factors, which have a ‘winged helix-turn-helix’ DNAbinding motif. GABPβ is a large protein that contains a
leucine zipper-like motif and a number of ankyrin
repeats, but it does not bind DNA directly. GABPβ binds
to the GABPα Ets motif and a C-terminal α helix using
the extended loop tips of its ankyrin repeats. GABPβ
Complexes of transactivation domains and
their target proteins
The complex structure of a CREB activation domain (the
phosphorylated kinase-inducible domain, pKID)
bound to its target (the KIX domain) on CBP has been
determined by NMR spectroscopy [12••]. Complex interactions between the herpes simplex virus protein-16
(VP16) activation domain and human TAF31 were also
characterized by an NMR study [13••]. More recently, the
crystal structure of the ligand-binding domain (LBD) of a
nuclear receptor, the peroxisome proliferator-activated
receptor-γ (PPAR-γ), which contains the activation function-2 (AF-2) motif, was determined in a ternary complex
with SRC-1 and the anti-diabetic ligand rosiglitazone
[14••,15••]. CBP, TAFs and SRC represent the major targets of transcription activators bound to upstream
enhancers. In both the pKID–KIX and the VP16–TAF
complexes, the transactivation domain presents an amphipathic α helix to a hydrophobic surface on their respective
target. These helices are flexible and largely unstructured
before binding. This flexibility may be important for the
binding of the same region in different conformations to
other regulatory proteins. In the pKID–KIX complex, a
phosphoserine at one end of the amphipathic helix plays
an important regulatory role, conveying the phosphorylation signal through a hydrogen bond interaction. In the
ternary complex of PPAR-γ LBD, rosiglitazone and SRC1, the coactivator SRC-1 displays an amphipathic helix to
a surface formed by AF-2 and other structural elements
from the nuclear receptor LBD. SRC-1 binding is ligand
dependent, providing another means of conveying a signal
to the transcription machinery.
Implications for the mechanisms of eukaryotic
transcription regulation
Together with biological studies on transcriptional synergy
or ‘cross talk’, what do the above complex structures tell us
about the combinatorial gene regulation mechanisms in
eukaryotic cells?
Members of a transcription factor family may be
differentiated in higher order transcription
factor complexes
In the higher order complex structures discussed above, the
residues of a DNA-binding domain that do not contact the
DNA mediate protein–protein interactions. Transcription factors from the same family usually have highly homologous
DNA-binding surfaces, but different surface residues outside
the DNA-binding region. There is some biological evidence
that these variable residues may be important determinants
of each family member’s distinct in vivo functions [33,34].
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Combinatorial gene regulation by eukaryotic transcription factors Chen
A sequence comparison of NFAT (NFATs 1–4) and Fos (cFos, FosB, Fra-1, Fra-2) family members indicated that
different NFAT–Fos pairs should have different interaction
interfaces [10••]. A similar specificity is also seen in the
MATα2–MATaa1–DNA complex, in which the MATα2 Cterminal α helix specifically binds to the MATaa1
homeodomain, but not its own homeodomain [25].
51
Figure 4
(a)
b
e
a
NFAT
RHR-C
The assembly of specific transcription factor complexes
contributes to the specificity of transcriptional control
For each individual transcription factor in the ternary
complexes discussed above, the homeodomain–DNA,
MADS box–DNA and Ets–DNA interactions are all similar to the interactions seen in their respective binary
protein–DNA complexes. This is true even when the
binding site deviates significantly from the consensus
sequence, as does DNA binding by Fos–Jun in the
NFAT–Fos–Jun complex. The recognition of nonconsensus sites by a transcription factor often involves only local
changes or adjustments of DNA-binding residues. Such
apparent ‘relaxation’ of specificity seems very common in
in vivo DNA binding by eukaryotic transcription factors,
especially as part of larger complexes. This may allow the
assembly of enhancer complexes on various composite
sites while maintaining the specificity by cooperative protein–protein interactions.
In higher order complexes, protein–protein interactions
add specificity to the combined DNA-binding specificity
of each component. In the MATα2–MATaa1–DNA and
MATα2–MCM1–DNA complexes, protein–protein interactions are mediated by structural modules that are
tethered to DNA-binding domains through a peptide linker. These linkers, though flexible in the crystal structures
(as evident from high B factors), still seem to impose specificity on complex formation by restricting the arrangement
of each component’s binding site [35]. In contrast, the
interactions between NFAT and Fos–Jun are directly
mediated by residues of their respective DNA-binding
domains and are continuous with the DNA-binding surfaces, similar to a nuclear receptor heterodimer–DNA
complex [36]. Thus, the whole complex has a continuous
DNA-binding groove, explaining why the spacing
between the NFAT and AP-1 DNA-binding sites is highly
conserved.
Significant conformational changes of the protein and
DNA are observed in the above higher order complexes
and they may play important roles in the specificity
(‘indirect read out’) and diversity of higher order complex
assembly. In the MATα2–MCM1–DNA complex, the
MATα2 linker contacting MCM1 shows flexibility by
being able to assume either a β strand or an α-helical conformation. Such flexibility may be important for MATα2
binding to a MCM1 dimer on both sides, with a two or
three base pair spacing on a natural a-specific operator
[9••]. The Fos α helix in the NFAT–Fos–Jun–DNA complex has a significant bend in its fork region. The fork
NFAT
RHR-N
(b)
NF-κB
RHR-C
a
b
e
NF-κB
RHR-N
Current Opinion in Structural Biology
Comparison of NFAT in the (a) NFAT–Fos–Jun–DNA complex and (b)
NF-κB p50 in the p50 dimer–DNA complex. The N-terminal DNAbinding domains of NFAT and p50 are similarly anchored on the DNA,
but their C-terminal domains are in very different orientations. The Cterminal domain of NFAT is similar to that of p50 (root mean square
deviation of 0.84 Å for 65 β strand Cα atoms, and most of the
dimerization residues at the abe sheet are conserved in NFAT).
region of DNA-bound bZIP proteins is usually flexible,
which may favor interactions with other proteins on
DNA, although it is not clear if members of the Fos family have different flexibility in this region or not. DNA
conformational changes in the NFAT–Fos–Jun complex
may explain why the DNA spacer between the NFAT
and AP-1 sites shows a strong preference for AT-rich
sequences [28].
Another level of specificity that is achieved through higher
order complex assembly is the specific orientation of heterodimeric DNA-binding proteins on DNA. Fos and Jun
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Protein–nucleic acid interactions
Figure 5
(b)
(a)
(c)
N
A
B
B
E
E
N
A
A
N
B
E
Minor groove
contact
C
ab loop
C
Minor groove
contact
Minor groove
contact
ab loop
ab loop
C
(d)
(e)
N
N
A
B
E
A
B
E
C
ab loop
ab loop
C
Minor groove contact
Current Opinion in Structural Biology
A comparison of the immunoglobulin DNA-binding domains of (a) p53,
(b) NFAT, (c) STAT, (d) NF-κB and (e) the T domain. The β barrel is
oriented similarly, with the ABE sheet shown in front. The conserved ab
loop bound in the DNA major groove is indicated. Note that in p53,
NFAT and STAT, the C-terminal α helix is positioned in the major
groove, whereas a β-strand loop is inserted in the adjacent minor
groove. The orientation of p53 on DNA is significantly different from
that of the others. NF-κB does not contact the DNA minor groove. A
C-terminal α helix of the T domain binds deeply in the minor groove,
opposite the groove contacted by p53, NFAT and STAT.
have almost identical DNA-binding surfaces. Their bZIP
heterodimer was found to bind DNA in two orientations in
the binary (Fos–Jun)–DNA complexes [37,38], but adopted
a unique orientation in the ternary NFAT–Fos–Jun–DNA
complex [37]. As seen in the ternary crystal structure [10••],
the NFAT–Fos and NFAT–Jun interaction interfaces are
different, leading to orientation specificity on the DNA.
Such a specific orientation of heterodimeric transcription
factors on DNA, either through their own asymmetric DNA
binding or through interactions with partner proteins, may
have functional importance.
without binding to DNA. As seen in the crystal structures,
the protein–protein interaction interfaces observed in
these complexes are either limited or highly hydrophilic.
This feature is also observed in other complexes, including
those of the signal transducer and activator of transcription
(STAT) proteins. Crystal structures of two STAT DNAbinding complexes and a STAT N-terminal domain have
been determined recently [39••,40••,41•]. DNA-bound
STAT dimers are suggested to form higher order complexes through the conserved N-terminal protein interaction
domain that probably only dimerizes after DNA binding.
The potential dimer interface of this STAT N-terminal
domain is highly hydrophilic, as seen in the crystallographic dimer [41•]. Complex formation between NFAT and
Fos–Jun, and between MATα2 and MATaa1 is also DNA-
Higher order complexes form upon DNA binding
Unlike many tightly associated transcription factor dimers,
most of the ternary complexes discussed above do not form
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Combinatorial gene regulation by eukaryotic transcription factors Chen
binding-dependent. This DNA-dependent complex formation may enable the combinatorial use of transcription
factors [25].
Combinatorial diversity is achieved at multiple levels
In addition to complex formation between distinct and
related transcription factors, the same DNA-binding
domain of a given transcription factor may adopt different
conformations in different promoter contexts, while
maintaining its specific DNA-binding interactions [42].
NFAT may be one example. On composite NFAT and
AP-1 DNA-binding sites, such as those found in the IL-2
promoter-enhancer, NFAT binds the DNA cooperatively
in complex with AP-1 transcription factors. On some
other DNA sites that have two NFAT DNA-binding sites
arranged with dyad symmetry and appropriate spacing,
NFAT binds the DNA cooperatively as a dimer. The latter mode of DNA binding by NFAT may be similar to
that of the Rel NF-KB transcription factors, which are
involved in a wide range of transcription regulation in the
immune system and in viral gene expression. The DNAbinding sites of the NFAT dimer resemble that of the
NF-KB proteins (the Kb DNA site), raising the possibility that NFAT may regulate gene transcription through
DNA sites (KB or KB-like DNA sites) that are also responsive towards NF-KB regulation. The structures of the
DNA-binding domains of NFAT and NF-KB are also
remarkably similar, both consisting of two Ig modules. In
the NFAT–Fos–Jun-DNA complex, each of NFAT’s two
Ig modules, Rel homology regions (RHRs) N and C,
resembles the corresponding parts of Rel NF-κB p50, but
the relative orientation of the two Ig modules in NFAT is
significantly different from that seen in p50–DNA complexes [43,44]. The C-terminal Ig module in p50
mediates dimer formation, whereas NFAT is a monomer
in solution [37,45] (Figure 4). Strikingly, residues
involved in p50 dimerization are largely conserved in the
NFAT C-terminal Ig module, suggesting that NFAT can
probably dimerize upon binding to DNA using the same
surface. There is evidence that NFAT may bind κB-like
DNA sites as a dimer under certain physiological situations [28], probably by adopting a conformation that is
very much like a typical NF-κB dimer (Figure 4).
Crystals of a NFAT dimer bound cooperatively to a κB
DNA fragment have been obtained and the structure
determination is underway (L Chen, A Breier, B Tasic,
SC Harrison, unpublished data). Alternatively, the
exposed NFAT C-terminal dimer interface can mediate
higher order complex formation between multiple copies
of DNA-bound NFAT–Fos–Jun complexes on an
enhancer [46], similar to the higher order assembly of
DNA-bound GABPβ/α and STAT dimers (see above).
The Ig DNA-binding domain is also found in a novel class
of transcription regulators, referred to as the T-domain
proteins. The T-domain proteins are the products of the
so-called T-box gene, which plays important roles in transcription regulation in embryonic development. The
53
recent structure determinations of NFAT, STATs and the
T-domain [47•] reveal that these proteins, together with
p53 [48] and NF-κB [43,44], form a superfamily that uses
the Ig module as a scaffold for presenting various secondary structural elements for DNA recognition
(Figure 5). Whether the above proteins are evolutionarily
related or not, however, is unclear at present. The recent
structure determination of a DNA-binding complex of
Skn-1 illustrated another way of generating diverse DNAbinding functions, combining various DNA-binding
motifs and scaffolds to form a novel DNA-binding domain
[49•]. This combination of DNA-binding modules is related to but is different from those seen in other
DNA-binding proteins, including zinc-finger proteins and
the POU domain proteins.
Transcriptional coactivators play important roles in the
combinatorial control of transcription
Considering the complexes between transactivation
domains and coactivators discussed above and similar
studies on p53 [50], it seems that the binding of transactivation domains to their target proteins generally involves
an induced amphipathic helix. This mode of protein–protein interaction is also seen in the MATα2–MATaa1–DNA
complex. Amphipathic helices have one or more φxxφφ
motifs, where φ represents a hydrophobic residue. In the
case of pKID, VP16 and other transactivation domains
(p53 and p65), the motif shows a preference for phenylalanine and tyrosine at the first φ, imposing some
specificity on coactivator selection. In SRC-1 and other
nuclear receptor coactivators, the motif is more restricted
to LXXLL (L represents leucine) [51]. The specificity of
coactivator binding also involves hydrogen bonding and
electrostatic interactions.
Thus, interactions between transactivation domains and coactivators are mediated by small, relatively independent
structural modules, each making limited but specific contacts.
There are three LXXLL motifs in SRC-1, two of which can
interact with a nuclear receptor dimer. The presence of a
third LXXLL may imply that these motifs can be used
either combinatorially with different nuclear receptor dimers
or simultaneously in forming higher order complexes.
Similarly, coactivators such as CBP and p300 also contain
separated binding sites for the transactivation domains of various transcription factors. These general features of
transactivation domain–coactivator interactions are consistent
with the combinatorial gene regulation mechanism.
Conclusions
In the past year, we have seen more structural characterizations of the protein–protein interactions involved in the
function of eukaryotic transcription factors. These include
the interactions between DNA-bound transcription factors and interactions between transactivation domains and
their respective targets. These structural studies support
the combinatorial transcription regulation mechanism in
eukaryotic cells.
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Protein–nucleic acid interactions
Structural studies of eukaryotic transcription factors with
higher and higher complexity continue. These structures
will allow the analysis of the molecular details of
enhancer complexes (enhanceosome), the core promoter
complex and the interactions between them. These molecular pictures will provide an important framework for
studying and understanding the in vivo mechanisms of
eukaryotic gene regulation.
Acknowledgements
The author is grateful to Ernest Fraenkel, Rachelle Gaudet, Susanne
Swalley and Marc Jacobs for critically reading this review and for their many
helpful comments. The author would like to thank Stephen C Harrison for
a wonderful postdoctoral experience in his laboratory. A postdoctoral
fellowship from the Medical Foundation is acknowledged.
References and recommended reading
Papers of particular interest, published within the annual period of review,
have been highlighted as:
• of special interest
•• of outstanding interest
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2.
Tan S, Richmond TJ: Eukaryotic transcription factors. Curr Opin
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3.
Tan S, Hunziker Y, Sargent DF, Richmond TJ: Crystal structure of a
yeast TFIIA/TBP/DNA complex. Nature 1996, 381:127-151.
4.
Geiger JH, Hahn S, Lee S, Sigler PB: Crystal structure of the yeast
TFIIA/TBP/DNA complex. Science 1996, 272:830-836.
5.
•
Shi Y, Wang YF, Jayaraman L, Yang H, Massague J, Pavletich NP:
Crystal structure of a Smad MH1 domain bound to DNA:
β signaling. Cell 1998,
insights on DNA binding in TGF-β
94:585-594.
This paper describes the first crystal structure of the DNA-binding domain
from a Smad family protein in complex with DNA, showing a novel
DNA-binding mode involving a β hairpin bound in the major groove.
6.
•
Escalante CR, Yie J, Thanos D, Aggarwal AK: Structure of IRF-1 with
bound DNA reveals determinants of interferon regulation. Nature
1998, 391:103-106.
The first crystal structure determination of a DNA-binding domain from the
interferon regulatory factor (IRF) family of proteins in complex with DNA,
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7.
Chen FE, Huang DB, Chen YQ, Ghosh G: Crystal structure of
κB bound to DNA.
p50/p65 heterodimer of transcription factor NF-κ
Nature 1998, 391:410-413.
12. Radhakrishnan I, Perez AG, Parker D, Dyson HJ, Montminy MR,
•• Wright PE: Solution structure of the KIX domain of CBP bound to
the transactivation domain of CREB: a model for
activator–coactivator interactions. Cell 1997, 91:741-752.
The first detailed structural characterization of the interactions between an
activation domain (CREB) and a coactivator (CBP).
13. Uesugi M, Nyanguile O, Lu H, Levine AJ, Verdine GL: Induced α helix
•• in the VP16 activation domain upon binding to a human TAF.
Science 1997, 277:1310-1313.
The first structural characterization of the interactions between VP16 and
TAF31, using NMR spectroscopy and biochemical methods.
14. Westin S, Kurokawa R, Nolte RT, Wisely GB, McInerney EM,
•• Rose DW, Milburn MV, Rosenfeld MG, Glass CK: Interactions
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15. Nolte RT, Wisely GB, Westin S, Cobb JE, Lambert MH, Kurokawa R,
•• Rosenfeld MG, Willson TM, Glass CK, Milburn MV: Ligand binding
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receptor-γγ. Nature 1998, 395:137-143.
This paper, together with [14••], describes the first crystallographic study of a
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