Transcription Factors / Overview 243

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TRANSCRIPTION FACTORS / Overview 243

TRANSCRIPTION FACTORS
Contents
Overview
AP-1
ATF
Fox
NF-jB and Ijb
POU
PU.1

Overview compatible with the DNA sequence with which they


must interact. After an initial contact is made, the
I M Adcock and K Ito, Imperial College London, protein and DNA come close enough together to
London, UK
form numerous atomic interactions. The atomic con-
G Caramori, University of Ferrara, Ferrara, Italy
tacts between protein and DNA are varied, including
& 2006 Elsevier Ltd. All rights reserved. hydrogen bonding, ionic interactions, and hydro-
phobic interactions. Activation of transcriptional en-
Abstract hancers appears to require the assembly of a highly
specific three-dimensional nucleoprotein complex
The term ‘transcription factor’ refers to a large family of pro-
involving extensive protein–DNA and protein–pro-
teins, which exert transcriptional control via specific interac-
tions with regulatory gene sequences. Here, we provide a tein interactions and the transcriptional efficiency of
summary of the different classes of the transcription factor di- these complexes can be altered by subtle changes
vided according to their DNA-binding motifs. The modular in the relative positions or orientations of proteins
structure of transcription factors and the presence of distinct within the complex. The comprehensive understand-
interacting domains determine the ability of these factors to
associate with each other and with coactivating/repressing pro-
ing of protein–DNA interactions requires the isola-
teins. By recruiting transcriptional coactivators, transcription tion of these complexes and X-ray crystallographic
factors can induce changes in chromatin structure enabling gene studies. However, the study of these proteins has
expression to occur. We use the activation of the Rel transcrip- been simplified by the recognition of common func-
tion factor NF-kB and the nuclear receptor GR as examples to tional and structural motifs within the many differ-
indicate some of the intricacies and subtleties of DNA binding,
ent proteins that recognize DNA (Table 1).
chromatin remodeling, and transcription factor cross-talk. Fi-
nally, we review the evidence for the involvement of select
transcription factors in allergic and inflammatory diseases of the
lung, and how changes in the expression and/or activity of these
factors may vary in disease and provide important targets for
future drug development. Table 1 Classification of transcription factors as structural
families

Domain Factors containing domain


Description and Definition Helix–loop–helix Homeodomain proteins
POU factors, e.g., Oct-1, Oct-2,
The production of messenger ribonucleic acid
Pit-1, Unc-86
(mRNA) from deoxyribonucleic acid (DNA) (tran- Zinc finger
scription) by a cell is strictly regulated. Transcrip- Cys-His Zn finger TFIIIA, Kruppel, Sp1
tional control results from the interaction between Cys-Cys Zn finger Nuclear hormone receptors, e.g.,
regulatory DNA sequences (promoters, enhancers, GR
Basic element
and silencers) and sequence-specific DNA-binding
Lucine zipper C/EBP, Fos, Jun, CREB, ATF2
proteins. The binding of these proteins to DNA se- Helix–loop–helix MyoD1, E12, E47
quences results in an increase or a decrease in the HTH þ ZIP Myc family proteins
transcription rate of the associated gene; thus, these b-Sheet Rel proteins, NF-kB
proteins are known as transcription factors. Proteins The large number of DNA-binding proteins can be grouped to-
recognize DNA in the same way as they recognize gether into a small number of families depending upon their
other proteins by forming a tertiary structure that is common structural motifs.
244 TRANSCRIPTION FACTORS / Overview

Generalized modular transcription factor

DNA binding Ligand-binding domain

HSP binding
Dimerization
NLS-1 NLS-2 Nuclear translocation
AD-1 AD-2 AD-3
Transactivation/
cofactor association
TF interaction
Figure 1 Modular structure of a generic transcription factor. The modular design of a transcription factor enables distinct regions of the
protein to function, in isolation, as ligand-binding domains, dimerization domains, nuclear localization domains, and transactivation and
transrepression (e.g., AP-1 and NF-kB interacting) domains. NLS, nuclear localization signal; AD-1/2/3, activating domain 1/2/3; TF-RE,
transcription factor response element.

Functional Domains Examples of these HTH transcription factors in-


clude the Drosophila homeotic genes and a variety of
Transcription factors are generally composed of seve-
mammalian proteins such as the Hox genes and thy-
ral domains possessing distinct functions such as
roid transcription factor-1 (TTF-1). Although an iso-
DNA binding, transactivator/repressor binding, and
lated homeodomain can fold correctly and bind
appropriate ligand binding (Figure 1). This modular
DNA with specificity similar to that of the intact
design with different functions in different domains is
protein, it seems likely that other regions of the pro-
a common theme in eukaryotic transcription factors,
tein modulate the precise DNA-binding specificity.
where the DNA-binding domains are only a part of
Protein–protein interactions with other transcription
the intact proteins. This domain structure is con- factors and general coactivators/repressors may also
served across species and can be interchanged or fused
have a role in modulating many homeodomain–
between transcription factors in experimental models,
DNA interactions and illustrate the important role
and often when this occurs in man in vivo, it can
that heterodimer formation can play in the regula-
result in disease, for example, in acute promyelocytic
tion of gene expression.
leukemia where fusion proteins between the retinoic
More recently, another class of regulatory protein
acid receptor alpha (RARa) and other transcription
has been identified in which the homeobox forms one
factors results in abnormal gene expression. In vitro,
part of the larger conserved domain known as the
interchanging a glucocorticoid receptor ligand-bind- POU domain, so called because it includes the pitu-
ing domain with a similar domain in the RARa gene,
itary specific protein Pit-1, the octamer binding
for example, results in glucocorticoids switching
proteins Oct-1 and Oct-2, and the nematode gene
on retinoic acid-regulated genes and retinoic acid-
unc-86 (Pit–Oct–Unc) domain to bind to DNA. The
modulating glucocorticoid-sensitive gene expression.
relative contribution of homeodomain and the POU-
specific domain differs between the different proteins
Structural Motifs with the homeodomain being sufficient for sequence-
specific binding of Pit-1, while both the homeodo-
Helix–Turn–Helix
main and the POU domain are necessary in the case
The helix–turn–helix (HTH) structure was the first of Oct-1.
DNA-recognition motif identified in which an a-heli- The high level of sequence similarity among dif-
cal region is followed by a sharp b-turn and then ferent homeoboxes predicts that the target DNA se-
another a-helical region. The proteins bind as dimers, quences of many of these proteins will be similar or
each monomer recognizing a half-site, and the ap- even identical, and indeed footprinting experiments
proximate symmetry of the DNA-binding site is re- have shown this to be the case. These observations
flected in the symmetry of the complexes. The first pose the important problem as to how proteins with
a-helical motif lies across the major groove of DNA similar DNA-binding specificities execute different
making hydrophobic interactions with the second regulatory roles.
helix, known as the recognition helix, which lies
partly within the major groove and makes specific
The Leucine Zipper and the Basic DNA-Binding
contact with DNA. The proteins are held in a stable
Domain (bZIP)
ordered manner by an extensive array of hydrogen
bonds. Mutations within this region allow dramatic The leucine zipper element is found in many trans-
changes in the specificity of DNA binding. cription factors throughout the animal kingdom,
TRANSCRIPTION FACTORS / Overview 245

such as the liver-specific transcription factor CCAAT/ new DNA-binding specificities and thus be targeted
enhancer binding protein (C/EBP) and the proto- to different sites than homodimers. In other cases,
oncogenes Myc, Fos, and Jun. In this structure, heterodimer formation may allow for different com-
leucine residues occur every seven amino acids in an binations of activation and/or repression domains
a-helical structure over 30–40 residues such that the and thus change the regulatory properties of a mol-
leucines occur every two turns on the same side of the ecule bound at a fixed DNA site.
helix. The leucine zipper facilitates the dimerization Although originally identified in leucine zipper-
of the protein by interdigitation of two leucine- containing proteins, the basic DNA-binding domain
containing helices on different molecules and these has also been identified by homology comparisons in
residues form the buried subunit interface of the a number of transcriptional regulatory proteins, such
coiled-coil dimer. In turn, such dimerization results in as MyoD1. In this case the basic domain is associated
the correct protein structure for DNA binding by the with an adjacent region that can form a helix–loop–
adjacent highly basic region that can interact directly helix structure in which two amphipathic helices
with the acidic DNA. This B30 residue basic region (containing all the charged residues on one side of
is rich in arginines and lysines, but also contains the helix) are separated by an intervening nonhelical
other residues that are conserved throughout the loop. This helix–loop–helix region acts in a manner
family or in particular subfamilies. bZIP proteins are analogous to that of the leucine zipper in that it al-
Y-shaped with the parallel leucine zipper region lows protein dimerization and hence DNA binding
forming the stem of the Y, and the basic region forms by the adjacent basic DNA-binding domain. Mem-
a-helices that extend off like the arms of the Y. The bers of the myc oncogene subfamily of DNA-binding
N-terminal end of the twofold symmetric leucine proteins contain both a leucine zipper and a helix–
zipper fits over the center of the DNA-binding site, loop–helix motif adjacent to the basic DNA region
and the helices from the basic region extend in op- suggesting that proteins containing the basic region
posite directions along the major grooves of the may form a related family comprised of three sub-
DNA. Transcription factors containing the basic groups containing a leucine zipper, an HTH motif, or
DNA-binding domain can only bind to DNA once both (Table 1).
they have formed transcription factor dimers. Hence,
factors containing the basic binding domain are fur-
b-Sheet Motifs
ther subgrouped according to the nature of the dime-
rization motif that they contain (Table 1). The Rel family of transcription factors are examples
Leucine zipper proteins can form heterodimers, of DNA-binding proteins with b-sheet motifs. Gen-
and these mixed dimers have important roles in the erally, leucine-rich repeats are short-sequence motifs
regulation of the biological activity of bZIP proteins. present in a number of proteins with diverse func-
Both Fos and Jun proteins, the major components of tions and cellular locations. All proteins containing
the transcription factor activator protein-1 (AP-1) these repeats are thought to be involved in protein–
bind to palindromic sequences in DNA known as protein interactions. Leucine-rich repeats correspond
TRE sites [TGAC/GTCA], which mediate gene in- to beta–alpha structural units arranged so that they
duction following phorbol ester treatment. Whilst form a parallel b-sheet with one surface exposed to
Jun can bind to DNA as a homodimer, Fos is unable the solvent, so that the protein acquires an unusual,
to homodimerize and cannot bind to DNA without nonglobular shape ideal for formation of specific
the formation of a Fos–Jun heterodimer. This differ- protein–protein interactions.
ence is due entirely to the differences in the leucine The X-ray crystallographic structure of some Rel
zippers of the two proteins since substitution of the proteins have been obtained and the Rel homology
Jun zipper region for that of the Fos zipper allows region (RHR) in the p50 nuclear factor kappa B (NF-
Fos homodimer formation and DNA binding kB) subunit consists of two flexibly linked domains,
through the basic region of Fos to occur. The re- each of which bears a remarkable similarity to an
quirement for dimer formation prior to DNA binding immunoglobulin domain. In its dimeric form bound
allows for regulatory control of AP-1 activity and to DNA, this RHR has the appearance of a butterfly.
thus gene expression. Although only the C-terminal domain contributes to
Heterodimers can also limit transcription factor the dimer interface, both domains are involved in
activity: the transcription factor cAMP response el- important DNA interactions. The p50 dimer wraps
ement binding protein (CREB), a cAMP response itself around two-thirds of the cylindrical DNA tube
regulator, is antagonized by formation of het- making 38 contacts and leaving only the minor
erodimers with cAMP response element modulator groove accessible. p50 interacts with DNA through
(CREM). In addition, heterodimers may also acquire loops on both the C-terminal dimerization domain
246 TRANSCRIPTION FACTORS / Overview

and the N-terminal domain. One of these loops in helix of each subunit fits into the major groove, and
the N-terminal domain of p50, the recognition side chains from this helix make contacts with the
loop, reaches into the DNA and contacts the bases. edges of the base pairs. The second major helix pro-
The proximity of DNA-binding residues to the dimer vides phosphate contacts with the DNA backbone
interface makes for a remarkably seamless set and provides the dimerization interface.
of protein–protein and protein–DNA contacts.
NF-kB binds to its consensus DNA sequence (50 -
GGGPuNNPyPyCC-30 ) with picomolar affinity com- Site-Specific Recognition
pared to the nanomolar affinity of most other
The intracellular control and regulation of gene ex-
DNA-binding proteins. The wrapping of the DNA
pression is mediated through complex interactions
and the large number of contacts with DNA accounts
between specific transcription factors and DNA con-
for this extraordinary affinity.
trol elements. Transcription factors can achieve rapid
target localization by initially binding to a non-
Zinc Fingers specific site on the DNA and then finding the specific
site by one-dimensional diffusion along the DNA, by
Zinc (Zn) finger proteins are involved in many as-
intersegment transfer, or both. Moreover, to over-
pects of eukaryotic gene regulation and occur in pro-
come binding to the vast excess of non-specific DNA
teins induced by differentiation and growth signals, in
and to ensure occupancy at the target sequence, spe-
proto-oncogenes, in general transcription factors, and
cific DNA-binding proteins must also distinguish be-
in regulatory genes of eukaryotic organisms. The
tween specific and non-specific DNA. The greater
DNA-binding region of these factors usually contains
affinity of these proteins for specific sites provides the
tandem repeats of the 30 residue zinc finger motif,
discrimination energy and thus determines their
Cys-X2/4-Cys-X12-His-X3–5-His. Therefore, each of
binding specificity.
these repeats contains two invariant pairs of cysteine
Recognition of the cognate binding sequence re-
and histidine residues, which coordinate a single
quires the formation of specific contacts between the
atom of zinc and hold the antiparallel b-sheet and a-
protein and the DNA and is often accompanied by
helices of the protein in a compact globular structure.
conformational changes in the protein, the DNA, or
This results in a finger-like structure that projects
both. Many DNA-binding proteins, especially tran-
from the surface of the protein. The tips of these fin-
scription regulatory proteins, induce DNA bending
gers make direct contact with the major groove of the
upon specific binding. The protein–DNA complex
DNA, alternate fingers binding on opposite sides of
requires 10–20 hydrogen bonds between the side
the helix. Examples of these types of transcription
chains of amino acids and with the DNA backbone.
factors include Sp1, the GATA family, and the Dro-
Most of these contacts are made by a-helical regions
sophila Kruppel gene. The zinc atom is essential for
within the protein motifs that fit into the major
DNA binding and the functioning of these transcrip-
groove, interacting with specific bases, especially
tion factors as mutation to remove zinc binding pro-
with purines, which are larger and offer more op-
duces effects identical to gene deletion.
portunities for hydrogen bonding. Folding and dock-
Nuclear hormone receptors are an important fam-
ing of the entire protein controls the meaning that
ily of regulatory proteins that includes the receptors
any particular side chain has in site-specific recogni-
for the hormones, retinoids, vitamin D, thyroid hor-
tion; furthermore, this recognition is a detailed struc-
mone, sex hormones (estrogens, progestins, and
tural process in which hydration may be important.
androgens), aldosterone, and glucocorticoids. These
Multiple DNA-binding domains are usually required
proteins contain separate regions for hormone bind-
for site-specific recognition. The same protein motifs,
ing, DNA binding, and for transcriptional activation.
such as Zn fingers or bZIP, may be used more than
The DNA-binding domains contain two zinc atoms,
once, as in binding by monomers and dimers, or
which are each held in place by four cysteine resi-
when a single polypeptide contains tandem repeat
dues. Therefore, this B70 amino acid region consists
motifs. Different motifs may also be used in the same
of two zinc fingers only as opposed to the multiple
transcriptional complex.
fingers (2–37) found in genes having Cys-His fingers
and are probably not evolutionarily related. The
DNA-binding domains from the glucocorticoid re-
Role of Transcription Factors in
ceptor and the estrogen receptor form two perpen-
Cell Regulation
dicular a-helices held together by hydrophobic
interactions and folded into a globular domain. The Cell growth, proliferation and differentiation are con-
glucocorticoid receptor binds as a dimer. The first trolled largely by selective transcriptional modulation
TRANSCRIPTION FACTORS / Overview 247

of gene expression in response to extracellular stim- precipitates the release of NF-kB from its inactive
uli. Much of this transcriptional control is governed state, enabling nuclear translocation and binding to
by the action of sequence-specific transcription fac- specific DNA response elements within the regula-
tors. In a similar manner, proinflammatory genes are tory regions of responsive genes.
stimulated following an inflammatory insult to the NF-kB is predominantly composed of the p50/p65
cell. Extracellular molecules interact with receptors heterodimer. Changes in p65 phosphorylation status
on the cell surface, which sets in motion coordinated can affect NF-kB function, for example, inactive p65
intracellular signaling cascades that cause the rapid is nonphosphorylated and is associated predomi-
transcriptional induction of selected genes. In the fi- nantly with the repressor protein histone deace-
nal steps of these cascades, many transcription factors tylases 1 (HDAC1), whereas p65 is phosphorylated
are phosphorylated and bind to sites in the control following IKK-2 stimulation and is able to bind to
regions of the required genes to stimulate their tran- coactivator molecules such as CREB-binding protein
scription. Interestingly, some transcription factors (CBP) and the related 300 kDa protein p300 (p300/
such as nuclear factor of activated T cells (NF-AT) CBP). Acetylation of p65 may also influence NF-kB
are dephosphorylated during activation. This binding function by affecting IkBa:p65 association and en-
of the phosphorylated/dephosphorylated activator hancing NF-kB activity.
must then be communicated to the basal transcrip-
tion machinery sitting some distance from the start Chromatin Modifications and Gene Expression
site of transcription.
DNA is tightly compacted around a protein core to
form nucleosomes, which are further compacted to
form chromatin. Each individual nucleosome con-
Proinflammatory Transcription Factors,
sists of B146 bp DNA associated with an octamer of
Chromatin Modifications, and Gene two molecules each of core histone proteins (H2A,
Transcription H2B, H3, and H4). Since the early 1960s, it has
Numerous transcription factors are activated during been known that the expression and repression of
the inflammatory response including ubiquitous fac- genes is associated with alterations in chromatin
tors such as AP-1 and NF-kB, cell-selective factors structure by enzymatic modification of core histones.
including GATA3, NF-ATs, and Forkhead (FOX) In the resting cell, DNA is tightly compacted around
proteins, and signal-selective factors such as signal these basic core histones, excluding the binding of
transducers and activators of transcription (STATs), the enzyme RNA polymerase II, which activates the
mothers against tetrapentaplegic (Smads), and C/EBP formation of mRNA. This conformation of the chro-
family members. In this overview we will discuss ac- matin structure is described as closed and is associ-
tivation of NF-kB and the glucocorticoid receptor ated with suppression of gene expression (Figure 2).
(GR) as an example of the general principles involved The irregular 30 nm chromatin fiber is stabilized
in transcription factor activation and signaling. NF- and further compacted by interactions between nuc-
kB is thought to be of paramount importance in leosomes and linker histones such as H1. Histone H1
asthmatic inflammation because it is activated by all has long been regarded as a general repressor of
the stimuli considered important in the inflammatory transcription, but there are indications that it also
response to allergen exposure and, in addition, it is has a role in transcriptional regulation. Here, histone
a major target for glucocorticoid action. NF-kB is
ubiquitously expressed within cells, and it not only
controls induction of inflammatory genes in its own RNA
polymerase II
right but also enhances the activity of other cell- and
signal-specific transcription factors.
X
NF-kB is activated by numerous extracellular
stimuli, including cytokines such as tumor necrosis 30 nm
factor (TNF)-a and interleukin (IL)-1b, viruses, some chromatin
fiber
bacteria, and allergens. Activation of cell-surface re-
ceptors leads to phosphorylation of receptor-associ-
ated kinases, which in turn phosphorylate the Figure 2 In the resting cell, DNA (gray bands) is tightly com-
inhibitors of NF-kB kinase (IKKs). Phosphorylation pacted around core histones to form nucleosomes. These nuc-
leosomes are further compacted to form a closed inaccessible
of IKKs results in phosphorylation of the NF-kB structure, excluding the binding of the enzyme RNA polymerase
cytoplasmic inhibitor (IkBa), so that IkBa is targe- II, which activates the formation of messenger RNA. This chro-
ted for proteosomal degradation. This degradation matin structure is associated with a lack of gene expression.
248 TRANSCRIPTION FACTORS / Overview

H1 acts as a ‘gate’ to nucleosomal DNA, preventing CBP, p300/CBP-associated factor (pCAF), and trans-
transcription factor DNA binding. Histone H1 re- criptional intermediary factor-2 (TIF-2). IL-1b can
moval is needed for opening factors to bind, thus also activate other pathways distinct from NF-kB
making nucleosomal DNA accessible to further tran- that can impinge on NF-kB activation. These
scription factor binding and transcription. Phosphor- additional pathways, such as protein kinase C and
ylation of histone H1 may play an essential role in nonreceptor tyrosine kinases, may enhance NF-kB
activation of gene transcription. activity, either by phosphorylating p65 and thereby
Specific residues (lysines, arginines, and serines) enhancing cofactor recruitment or by phosphoryla-
within the N-terminal tails are capable of being ting NF-kB-associated cofactors.
posttranslationally modified by acetylation, methyl-
ation, ubiquitination, or phosphorylation, all of
Temporal Association of NF-jB with DNA,
which have been implicated in the regulation of gene
Cofactors, and Gene Induction
expression. Acetylation of the s-group on lysines re-
duces the charge of the histone residue and subse- The simplistic model described above does not ex-
quently releases the tightly wound DNA, allowing the plain all aspects of NF-kB action, however. Immedi-
recruitment of further large protein complexes. A ate early genes such as IkBa do indeed bind NF-kB
breakthrough in the discovery of the role of histone to their promoters rapidly after lipopolysaccharide
acetylation was the demonstration that transcrip- (LPS) stimulation, but within 10 min NF-kB dissoci-
tional coactivators such as CBP and p300/CBP- ates from the IkBa promoter site and never reasso-
associated factor (pCAF) have intrinsic histone ciates. In contrast, NF-kB binds to its promoter sites
acetyltransferase (HAT) activity, which is activated in DNA for up to 2 h before dissociation in distinct
by the binding of transcription factors such as NF-kB. sets of genes (such as manganese superoxide di-
Increased gene transcription is therefore associated smutase and macrophage inflammatory protein-2), in
with an increase in histone acetylation, whereas spite of stimulation by LPS at the same time. How-
hypoacetylation is correlated with reduced transcrip- ever, other NF-kB-regulated genes, such as the
tion or gene silencing. Histone acetylation is an ac- chemokines/cytokines RANTES (regulated on acti-
tive process whereby small changes in the activity of vation, normal T cell expressed and % secreted), mon-
%
HATs or histone deacetylases (HDACs) can mark- % % % %
ocyte chemoattractant protein-1, and IL-6, do not
edly affect the overall histone acetylase activity as- show NF-kB binding to their promoters until 2 h af-
sociated with inflammatory genes. Importantly, these ter activation. NF-kB sites in the promoter regions of
changes in histone acetylation appear to be targeted these genes are originally in a repressed chromatin
toward regions of DNA associated with specific ac- environment that prevents NF-kB DNA binding and
tivator sites within the regulatory regions of induced subsequent gene expression. These become accessible
inflammatory genes, although a global loosening of only after AP-1-mediated histone acetylation and
histone structure has also been proposed. Under rest- subsequent alteration in the local nucleosomal struc-
ing conditions, less than half of the potential lysine ture (chromatin remodeling) (Figure 3). Thus, there
residues available for acetylation are in fact acety- are subtle changes in NF-kB DNA binding that are
lated, and these residues have a rapid turnover. This promoter context-dependent, precede coactivator re-
situation suggests that even small changes above or cruitment, and are not detectable using conventional
below the resting level are enough to lead to an ac- band shift and reporter gene assays. The question as
tivated chromatin state. This model predicts that to which aspect of chromatin changes occurs first,
changes in the ‘histone code’, the diverse range of remodeling or modification, prior to gene induction
histone tail posttranslational modifications such is still a matter of intense debate.
as acetylation, methylation, phosphorylation, and The question arises: how can NF-kB, or any other
ubiquitination that are set and maintained by his- transcription factor, interact with its recognition site
tone-modifying enzymes, must be translated into when DNA is compacted? NF-kB may bind to a kB-
downstream events extremely rapidly. RE within the linker DNA between nucleosomes
or, alternatively, when the kB-RE core residues are
facing outward from the DNA wrapped around hi-
NF-jB Activation Induces Histone Acetylation
stones. Binding to the kB-RE may then modify the
NF-kB can induce acetylation on both histone H3 local chromatin structure or cause local histone
and H4 in both a time- and concentration-dependent modifications altering NF-kB access to the promoter
manner depending upon the stimulus and the cell site. High-resolution mapping of GR interactions
type involved following the recruitment of a large with a glucocorticoid-responsive promoter suggests
coactivator complex that contains the HAT proteins that the GR not only reorganizes the chromatin
TRANSCRIPTION FACTORS / Overview 249

TF1 HATs
txn

TF1 responsive promoter


Modification/remodeling
(a)

TF1 TF2 SWI/SNF TF1 HATs


+ ATP
No txn X No txn txn
X

Remodeling
Modification/remodeling
TF1 responsive promoter
(b)
Figure 3 Temporal activation of inflammatory genes. (a) Simple model of transcription factor (TF1) activation of immediate early
response genes. Activation of TF1 by exogenous stimuli results in TF1 binding to TF1-response (RE)-sites in the regulatory regions of
the immediate early response genes, subsequent recruitment of HATs, and chromatin modification, leading to chromatin remodeling and
induction of gene transcription (txn). Often in the case of these genes, TF1 is rapidly ejected from DNA within 10 min. (b) A more complex
model accounts for the fact that many genes do not show TF1 promoter binding for up to 2 h following stimulation of TF1 activation, and
no transcription of these genes occurs during this time. Transcription requires binding of another TF, TF2, binding to its consensus site
within the gene regulatory domain and subsequent ATP-dependent chromatin remodeling using the SWI/SNF complex to reveal the TF1
DNA-binding site. Once the regulatory regions are remodeled, TF1 is able to bind to DNA, recruit HATs, and drive gene expression.

immediately surrounding its binding site but can also p65, there is a ‘hit-and-run’ mechanism of action
have effects elsewhere, thereby enforcing a particular rather than a stable association with glucocorticoid
translational frame on the chromatin template and response element (GRE). GR resides on DNA for less
modifying the effects of other DNA-binding proteins. than 10 s before being ejected and replaced by
another GR. This ejection may allow binding of ad-
ditional regulatory factors that enhance gene tran-
Ordered Recruitment of Coactivator Complexes
scription, such as HAT-containing complexes, and
One other important question that also needs to be may also play a role in feedback regulation. Inter-
addressed is whether there is a specific order of re- estingly, in the absence of ATP and chromatin
cruitment of distinct coactivator factors to the acti- remodeling factors, the GR stably interacts with
vated DNA-bound NF-kB complex to enable gene glucocorticoid-responsive genes.
transcription. Recent work examining androgen and
thyroid hormone receptor gene activation shows that
Cross-Talk between Transcription
nuclear hormone receptors do not in themselves
Factors and Their Transduction Pathways
recruit all the cofactors required at the target pro-
moters. Steroid receptor coactivators, recruited by The complexity of transcription factor activation
receptors, can in turn recruit other coactivators such pathways and their ability to engage in cross-talk
as p300/CBP, which can subsequently recruit SWI/ may enable cells to overcome inhibition of one path-
SNF (a large multisubunit protein complex) and way and retain a capacity to activate specific inflam-
mediator complexes. SWI/SNF enables chromatin matory genes. Generally, it is necessary to have
remodeling to occur in an adenosine triphosphate coordinate activation of several transcription factors
(ATP)-dependent manner, but histone acetylation by in order to have maximal gene expression. This may
p300/CBP facilitates the recruitment of SWI/SNF and explain how ubiquitous transcription factors may
mediator complexes. Thus, cofactor–cofactor inter- regulate specific genes in certain types of cells only.
actions are essential for effective gene expression. Activation of NF-kB leads to the coordinated induc-
The interactions do not have to occur sequentially, tion of multiple inflammatory and immune genes.
but histone acetylation can enhance the recruitment Whilst NF-kB is not the only transcription factor in-
of large multiprotein complexes in a coordinated volved in regulation of these genes, it often appears
manner. to have a decisive role often in cooperation with
However, again the story is found to be more other transcription factors such as AP-1 and C/EBP.
complex. In some cases, such as the GR and possibly The role of NF-kB should be seen as an amplifying
250 TRANSCRIPTION FACTORS / Overview

and perpetuating mechanism that will exaggerate polarization, respectively, by acting both on regu-
the disease-specific inflammatory process through the lated gene expression and by epigenetic control. For
coordinated activation of multiple inflammatory example, GATA-3 seems to be of particular impor-
genes. tance in the differentiation of human Th2 cells and
The fact that many inflammatory genes, which also the suppression of Th1 cytokine production by
are regulated by AP-1, NF-kB, and C/EBP, can be resetting the Th1 and Th2 gene loci. T-bet performs a
downregulated by glucocorticoids indicates the pos- similar function for Th1 differentiation and cytokine
sible importance of cross-talk between these signal production. GATA-3 expression is increased in the
transduction pathways. For example, activation of peripheral venous blood T cells from atopic asth-
the IL-8 promoter by NF-kB and C/EBP is inhibited matics and in induced sputum cells from asthmatic
by dexamethasone primarily via the NF-kB site. subjects particularly after allergen challenge and
Conversely, activation of a GRE-dependent promoter T-bet appears to be overexpressed in Th1 diseases.
by dexamethasone was inhibited by overexpression Understanding of the molecular mechanisms for
of p65. These and other studies show direct protein– Th1 and Th2 cytokine production developed in an-
protein interactions between NF-kB and GR, which imal models predicts that altered expression of
prevent NF-kB transactivation and partly account for STAT4 and STAT6 would be found in allergic air-
the anti-inflammatory properties of glucocorticoids. way disease. Despite convincing data in disease mod-
GR represses AP-1 transactivation using mechanisms els, this has not been confirmed in man. Interestingly,
similar to those used to inhibit NF-kB activation. enhanced activation of STAT1 has been reported in
the airways of patients with asthma and in subjects
with cystic fibrosis. Protein inhibitor of activated
Transcription Factors in Lung Disease
STAT1 (PIAS1) has also been implicated as playing a
There has been a recent increase in the number of role in the pathogenesis of cystic fibrosis. Sp1 is a
investigations of transcription factor activity and/or ubiquitous transcription factor that binds to GC-
expression in human respiratory diseases to provide boxes and related motifs, which are frequently oc-
proof of concept and validation for murine disease curring DNA elements present in many promoters
models. Many transcription factors such as p53, and enhancers. Modification of these sites within the
TTF-1, early growth response-1 (Egr-1), STAT3, in- IL-4, IL-10, and 5-lipoxygenase promoters has been
sulin-derived growth factor (IGF), and RARs are in- associated with altered expression of these genes in
volved in the pathogenesis of lung carcinoma. In distinct groups of asthmatic patients.
addition, NF-kB also appears to play a critical role in The expression of the GR has been examined in
resistance to chemotherapy, inhibition of tumorigen- several steroid-sensitive and -insensitive respiratory
esis, and the induction of anti-apoptotic genes. diseases. GRa expression has been reported to be
NF-kB has been implicated in most, if not all, in- lower in steroid-insensitive interstitial pulmonary fi-
flammatory diseases and diseases of the lung are no brosis (IPF) than in steroid-sensitive diseases such as
exception. For example, NF-kB activity is enhanced sarcoidosis and cryptogenic organizing pneumonia
in asthma, chronic obstructive pulmonary disease (COP). In contrast, no changes in GRa expression
(COPD), cystic fibrosis, and mineral dust diseases. It have been reported in severe therapy-insensitive
has been suggested that cystic fibrosis transmem- asthma and determination of GRa expression in
brane regulator (CFTR) acts as a pattern recognition COPD has not yet been reported. Changes in the
receptor regulating NF-kB activity and the D508 expression of GRb, a dominant negative form of GR,
mutation leads to constitutive NF-kB activation. do not appear to correlate with steroid sensitivity in
Furthermore, hepatic nuclear factor (HNF)-1 confers most lung diseases although this remains controver-
tissue-selective expression of CFTR. sial for severe asthma. Furthermore, abnormal
In addition, there is evidence for increased expres- expression of other nuclear hormone receptors in-
sion of c-Fos in bronchial epithelial cells in asthmatic cluding peroxisome proliferating antigen receptor
airways, and many of the stimuli relevant to asthma (PPAR)g and the vitamin D3 receptor (VD3R) has
that activate NF-kB will also activate AP-1. In ad- been reported in BAL macrophages and T cells in
dition, enhanced activity of both NF-kB and AP-1 patients with sarcoidosis. Importantly, recent evi-
has been reported in the airways of severe therapy- dence suggests that a dysfunctional interaction be-
insensitive asthmatic patients. In addition, a recent tween GR and C/EBPa in airway smooth muscle cells
study showed a genetic association of asthma sever- plays a role in their increased proliferation seen in
ity with the zinc finger transcription factor PHF11. the lower airways of asthmatics and might explain
Two transcription factors GATA-3 and T-bet why this is not affected by treatment with inhaled
appear to be critically important for Th2 and Th1 corticosteroids.
TRANSCRIPTION FACTORS / AP-1 251

There is also evidence for activation of NF-kB in See also: Corticosteroids: Glucocorticoid Receptors.
the bronchial epithelial cells of patients with COPD Transcription Factors: AP-1; ATF; Fox; NF-kB and Ikb;
and in the sputum macrophages during COPD ex- POU; PU.1.
acerbations. Finally, there is an increased number of
activated STAT4þ cells in the bronchial biopsies of Further Reading
smokers with mild–moderate COPD compared with
Andersen B and Rosenfeld MG (2001) POU domain factors in the
smokers with normal lung function. The presence of neuroendocrine system: lessons from developmental biology
activated STAT4þ cells is significantly associated provide insights into human disease. Endocrinology Review 22:
with the presence of IFN-gþ cells in both bronchial 2–35.
biopsies and bronchoalveolar lavage-derived lympho- Barnes PJ and Adcock IM (2003) How do corticosteroids work in
cytes and correlates with the degree of airflow limi- asthma? Annals of Internal Medicine 139: 359–370.
Caramori G, Ito K, and Adcock IM (2004) Transcription factors in
tation in smokers.
asthma and COPD. I Drugs 7: 764–770.
Transforming growth factor beta (TGF-b) is pos- Escoubet-Lozach L, Glass CK, and Wasserman SI (2002) The role
tulated to play a major role in several lung diseases of transcription factors in allergic inflammation. Journal of
where airway remodeling has been implicated, such Allergy and Clinical Immunology 110: 553–564.
as asthma, COPD, and fibrosing lung disease. TGF-b Ghosh S and Karin M (2002) Missing pieces in the NF-kappaB
puzzle. Cell 109(supplement): S81–S96.
stimulates a family of transcription factors known
Groneberg DA, Witt H, Adcock IM, Hansen G, and Springer J
as Smads. The Smad family consists of the receptor- (2004) Smads as intracellular mediators of airway inflammation.
regulated Smads (R-Smads), a common pathway Experimental Lung Research 30: 223–250.
Smad (co-Smad), and inhibitory Smads (anti-Smads). Hermanson O, Glass CK, and Rosenfeld MG (2002) Nuclear re-
R-Smads include Smads 1, 2, 3, 5, 8, and 9 and are ceptor coregulators: multiple modes of modification. Trends in
Endocrinology and Metabolism 13: 55–60.
phosphorylated following TGF-b receptor binding.
Latchman DS (1999) Eukaryotic Transcription Factors, 3rd edn.
Smad4 is a co-Smad and is not phosphorylated by the Oxford: Academic Press.
TGF-b receptor binding. Anti-Smads include Smad6 Pabo CO and Sauer RT (1992) Transcription factors: structural
and Smad7, which downregulate TGF-b receptor families and principles of DNA recognition. Annual Review of
signaling. Recent reports suggest that the expression Biochemistry 61: 1053–1095.
Sharrocks AD (2001) The ETS-domain transcription factor family.
of the inhibitory SMADs 6 and 7 are significantly
Nature Review of Cellular and Molecular Biology 2: 827–837.
downregulated in COPD. In addition, abnormal Sirulnik A, Melnick A, Zelent A, and Licht JD (2003) Molecular
Smad3 expression has been reported in pulmonary pathogenesis of acute promyelocytic leukaemia and APL vari-
hypertension and cystic fibrosis. Fibrosis has also ants. Best Practice and Research in Clinical Haematology 16:
been associated with changes in hypoxia and specifi- 387–408.
Urnov FD and Wolffe AP (2001) Chromatin remodeling and tran-
cally hypoxia-inducible factor (HIF)-1 and more
scriptional activation: the cast (in order of appearance). Onco-
general redox-sensitive transcription factors such as gene 20: 2991–3006.
NF-kB and AP-1. Data from animal models have also White RJ (2001) Gene Transcription: Mechanisms and Control.
implicated a role for factors such as Thy1 and NRF2, Oxford: Blackwell.
although their role in human disease awaits confir-
mation. In addition, aberrant epithelial cell regener-
ation characteristic of IPF has been associated with
increased expression of p53, b-catenin/Wnt, and
deltaNp63. AP-1
Studies of transcription factor interactions may
E Shaulian, Hebrew University Medical School,
thus have therapeutic potential in the control of
Jerusalem, Israel
many lung diseases. Glucocorticoids are the most
effective treatment for asthma and exert their & 2006 Elsevier Ltd. All rights reserved.
anti-inflammatory effects largely by binding to trans-
cription factors that have been activated by inflam- Abstract
matory cytokines. Other drugs that regulate the
The AP-1 transcription factor is a dimeric transcription factor
activity of specific transcription factors may also be composed of proteins from several families including Jun,
developed in the future. The identification of enzyme Fos, ATF, and Maf. AP-1 regulates various cell-autonomous as
targets, such as Jun kinases or IKKs, may also lead to well as general physiological and pathological effects. This
the development of new drugs that are able to con- review describes the proteins making up AP-1, briefly mentions
trol oncogenesis and/or inflammation. Cell-specific the diverse mechanisms by which the expression and activity
of its components are regulated, and categorizes the major
transcription factors may be a more attractive target, types of genes regulated by it. The experimental evidence impli-
as this may lead to the development of drugs with a cating AP-1 in different processes such as proliferation, differ-
reduced risk of adverse effects. entiation, apoptosis, migration and wound healing, malignant

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