TRANSCRIPTION FACTORS / Overview 243
TRANSCRIPTION FACTORS
Contents
Overview
AP-1
ATF
Fox
NF-jB and Ijb
POU
PU.1
Overview
I M Adcock and K Ito, Imperial College London,
London, UK
G Caramori, University of Ferrara, Ferrara, Italy
& 2006 Elsevier Ltd. All rights reserved.
Abstract
The term ‘transcription factor’ refers to a large family of pro-
teins, which exert transcriptional control via specific interac-
tions with regulatory gene sequences. Here, we provide a
summary of the different classes of the transcription factor di-
vided according to their DNA-binding motifs. The modular
structure of transcription factors and the presence of distinct
interacting domains determine the ability of these factors to
associate with each other and with coactivating/repressing pro-
teins. By recruiting transcriptional coactivators, transcription
factors can induce changes in chromatin structure enabling gene
expression to occur. We use the activation of the Rel transcrip-
tion factor NF-kB and the nuclear receptor GR as examples to
indicate some of the intricacies and subtleties of DNA binding,
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.
Description and Definition
The production of messenger ribonucleic acid
(mRNA) from deoxyribonucleic acid (DNA) (tran-
scription) by a cell is strictly regulated. Transcrip-
tional control results from the interaction between
regulatory DNA sequences (promoters, enhancers,
and silencers) and sequence-specific DNA-binding
proteins. The binding of these proteins to DNA se-
quences results in an increase or a decrease in the
transcription rate of the associated gene; thus, these
proteins are known as transcription factors. Proteins
recognize DNA in the same way as they recognize
other proteins by forming a tertiary structure that is
compatible with the DNA sequence with which they
must interact. After an initial contact is made, the
protein and DNA come close enough together to
form numerous atomic interactions. The atomic con-
tacts between protein and DNA are varied, including
hydrogen bonding, ionic interactions, and hydro-
phobic interactions. Activation of transcriptional en-
hancers appears to require the assembly of a highly
specific three-dimensional nucleoprotein complex
involving extensive protein–DNA and protein–pro-
tein interactions and the transcriptional efficiency of
these complexes can be altered by subtle changes
in the relative positions or orientations of proteins
within the complex. The comprehensive understand-
ing of protein–DNA interactions requires the isola-
tion of these complexes and X-ray crystallographic
studies. However, the study of these proteins has
been simplified by the recognition of common func-
tional and structural motifs within the many differ-
ent proteins that recognize DNA (Table 1).
Table 1 Classification of transcription factors as structural
families
Domain Factors containing domain
Helix–loop–helix Homeodomain proteins
POU factors, e.g., Oct-1, Oct-2,
Pit-1, Unc-86
Zinc finger
Cys-His Zn finger TFIIIA, Kruppel, Sp1
Cys-Cys Zn finger Nuclear hormone receptors, e.g.,
GR
Basic element
Lucine zipper C/EBP, Fos, Jun, CREB, ATF2
Helix–loop–helix MyoD1, E12, E47
HTH þ ZIP Myc family proteins
b-Sheet Rel proteins, NF-kB
The large number of DNA-binding proteins can be grouped to-
gether into a small number of families depending upon their
common structural motifs.
244 TRANSCRIPTION FACTORS / Overview
Generalized modular transcription factor
DNA binding
NLS-1
AD-1 AD-2
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
Transcription factors are generally composed of seve-
ral domains possessing distinct functions such as
DNA binding, transactivator/repressor binding, and
appropriate ligand binding (Figure 1). This modular
design with different functions in different domains is
a common theme in eukaryotic transcription factors,
where the DNA-binding domains are only a part of
the intact proteins. This domain structure is con-
served across species and can be interchanged or fused
between transcription factors in experimental models,
and often when this occurs in man in vivo, it can
result in disease, for example, in acute promyelocytic
leukemia where fusion proteins between the retinoic
acid receptor alpha (RARa) and other transcription
factors results in abnormal gene expression. In vitro,
interchanging a glucocorticoid receptor ligand-bind-
ing domain with a similar domain in the RARa gene,
for example, results in glucocorticoids switching
on retinoic acid-regulated genes and retinoic acid-
modulating glucocorticoid-sensitive gene expression.
Structural Motifs
Helix–Turn–Helix
The helix–turn–helix (HTH) structure was the first
DNA-recognition motif identified in which an a-heli-
cal region is followed by a sharp b-turn and then
another a-helical region. The proteins bind as dimers,
each monomer recognizing a half-site, and the ap-
proximate symmetry of the DNA-binding site is re-
flected in the symmetry of the complexes. The first
a-helical motif lies across the major groove of DNA
making hydrophobic interactions with the second
helix, known as the recognition helix, which lies
partly within the major groove and makes specific
contact with DNA. The proteins are held in a stable
ordered manner by an extensive array of hydrogen
bonds. Mutations within this region allow dramatic
changes in the specificity of DNA binding.
Ligand-binding domain
HSP binding
Dimerization
NLS-2 Nuclear translocation
AD-3
Transactivation/
cofactor association
TF interaction
Examples of these HTH transcription factors in-
clude the Drosophila homeotic genes and a variety of
mammalian proteins such as the Hox genes and thy-
roid transcription factor-1 (TTF-1). Although an iso-
lated homeodomain can fold correctly and bind
DNA with specificity similar to that of the intact
protein, it seems likely that other regions of the pro-
tein modulate the precise DNA-binding specificity.
Protein–protein interactions with other transcription
factors and general coactivators/repressors may also
have a role in modulating many homeodomain–
DNA interactions and illustrate the important role
that heterodimer formation can play in the regula-
tion of gene expression.
More recently, another class of regulatory protein
has been identified in which the homeobox forms one
part of the larger conserved domain known as the
POU domain, so called because it includes the pitu-
itary specific protein Pit-1, the octamer binding
proteins Oct-1 and Oct-2, and the nematode gene
unc-86 (Pit–Oct–Unc) domain to bind to DNA. The
relative contribution of homeodomain and the POU-
specific domain differs between the different proteins
with the homeodomain being sufficient for sequence-
specific binding of Pit-1, while both the homeodo-
main and the POU domain are necessary in the case
of Oct-1.
The high level of sequence similarity among dif-
ferent homeoboxes predicts that the target DNA se-
quences of many of these proteins will be similar or
even identical, and indeed footprinting experiments
have shown this to be the case. These observations
pose the important problem as to how proteins with
similar DNA-binding specificities execute different
regulatory roles.
The Leucine Zipper and the Basic DNA-Binding
Domain (bZIP)
The leucine zipper element is found in many trans-
cription factors throughout the animal kingdom,

such as the liver-specific transcription factor CCAAT/
enhancer binding protein (C/EBP) and the proto-
oncogenes Myc, Fos, and Jun. In this structure,
leucine residues occur every seven amino acids in an
a-helical structure over 30–40 residues such that the
leucines occur every two turns on the same side of the
helix. The leucine zipper facilitates the dimerization
of the protein by interdigitation of two leucine-
containing helices on different molecules and these
residues form the buried subunit interface of the
coiled-coil dimer. In turn, such dimerization results in
the correct protein structure for DNA binding by the
adjacent highly basic region that can interact directly
with the acidic DNA. This B30 residue basic region
is rich in arginines and lysines, but also contains
other residues that are conserved throughout the
family or in particular subfamilies. bZIP proteins are
Y-shaped with the parallel leucine zipper region
forming the stem of the Y, and the basic region forms
a-helices that extend off like the arms of the Y. The
N-terminal end of the twofold symmetric leucine
zipper fits over the center of the DNA-binding site,
and the helices from the basic region extend in op-
posite directions along the major grooves of the
DNA. Transcription factors containing the basic
DNA-binding domain can only bind to DNA once
they have formed transcription factor dimers. Hence,
factors containing the basic binding domain are fur-
ther subgrouped according to the nature of the dime-
rization motif that they contain (Table 1).
Leucine zipper proteins can form heterodimers,
and these mixed dimers have important roles in the
regulation of the biological activity of bZIP proteins.
Both Fos and Jun proteins, the major components of
the transcription factor activator protein-1 (AP-1)
bind to palindromic sequences in DNA known as
TRE sites [TGAC/GTCA], which mediate gene in-
duction following phorbol ester treatment. Whilst
Jun can bind to DNA as a homodimer, Fos is unable
to homodimerize and cannot bind to DNA without
the formation of a Fos–Jun heterodimer. This differ-
ence is due entirely to the differences in the leucine
zippers of the two proteins since substitution of the
Jun zipper region for that of the Fos zipper allows
Fos homodimer formation and DNA binding
through the basic region of Fos to occur. The re-
quirement for dimer formation prior to DNA binding
allows for regulatory control of AP-1 activity and
thus gene expression.
Heterodimers can also limit transcription factor
activity: the transcription factor cAMP response el-
ement binding protein (CREB), a cAMP response
regulator, is antagonized by formation of het-
erodimers with cAMP response element modulator
(CREM). In addition, heterodimers may also acquire
TRANSCRIPTION FACTORS / Overview 245
new DNA-binding specificities and thus be targeted
to different sites than homodimers. In other cases,
heterodimer formation may allow for different com-
binations of activation and/or repression domains
and thus change the regulatory properties of a mol-
ecule bound at a fixed DNA site.
Although originally identified in leucine zipper-
containing proteins, the basic DNA-binding domain
has also been identified by homology comparisons in
a number of transcriptional regulatory proteins, such
as MyoD1. In this case the basic domain is associated
with an adjacent region that can form a helix–loop–
helix structure in which two amphipathic helices
(containing all the charged residues on one side of
the helix) are separated by an intervening nonhelical
loop. This helix–loop–helix region acts in a manner
analogous to that of the leucine zipper in that it al-
lows protein dimerization and hence DNA binding
by the adjacent basic DNA-binding domain. Mem-
bers of the myc oncogene subfamily of DNA-binding
proteins contain both a leucine zipper and a helix–
loop–helix motif adjacent to the basic DNA region
suggesting that proteins containing the basic region
may form a related family comprised of three sub-
groups containing a leucine zipper, an HTH motif, or
both (Table 1).
b-Sheet Motifs
The Rel family of transcription factors are examples
of DNA-binding proteins with b-sheet motifs. Gen-
erally, leucine-rich repeats are short-sequence motifs
present in a number of proteins with diverse func-
tions and cellular locations. All proteins containing
these repeats are thought to be involved in protein–
protein interactions. Leucine-rich repeats correspond
to beta–alpha structural units arranged so that they
form a parallel b-sheet with one surface exposed to
the solvent, so that the protein acquires an unusual,
nonglobular shape ideal for formation of specific
protein–protein interactions.
The X-ray crystallographic structure of some Rel
proteins have been obtained and the Rel homology
region (RHR) in the p50 nuclear factor kappa B (NF-
kB) subunit consists of two flexibly linked domains,
each of which bears a remarkable similarity to an
immunoglobulin domain. In its dimeric form bound
to DNA, this RHR has the appearance of a butterfly.
Although only the C-terminal domain contributes to
the dimer interface, both domains are involved in
important DNA interactions. The p50 dimer wraps
itself around two-thirds of the cylindrical DNA tube
making 38 contacts and leaving only the minor
groove accessible. p50 interacts with DNA through
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

of gene expression in response to extracellular stim-
uli. Much of this transcriptional control is governed
by the action of sequence-specific transcription fac-
tors. In a similar manner, proinflammatory genes are
stimulated following an inflammatory insult to the
cell. Extracellular molecules interact with receptors
on the cell surface, which sets in motion coordinated
intracellular signaling cascades that cause the rapid
transcriptional induction of selected genes. In the fi-
nal steps of these cascades, many transcription factors
are phosphorylated and bind to sites in the control
regions of the required genes to stimulate their tran-
scription. Interestingly, some transcription factors
such as nuclear factor of activated T cells (NF-AT)
are dephosphorylated during activation. This binding
of the phosphorylated/dephosphorylated activator
must then be communicated to the basal transcrip-
tion machinery sitting some distance from the start
site of transcription.
Proinflammatory Transcription Factors,
Chromatin Modifications, and Gene
Transcription
Numerous transcription factors are activated during
the inflammatory response including ubiquitous fac-
tors such as AP-1 and NF-kB, cell-selective factors
including GATA3, NF-ATs, and Forkhead (FOX)
proteins, and signal-selective factors such as signal
transducers and activators of transcription (STATs),
mothers against tetrapentaplegic (Smads), and C/EBP
family members. In this overview we will discuss ac-
tivation of NF-kB and the glucocorticoid receptor
(GR) as an example of the general principles involved
in transcription factor activation and signaling. NF-
kB is thought to be of paramount importance in
asthmatic inflammation because it is activated by all
the stimuli considered important in the inflammatory
response to allergen exposure and, in addition, it is
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
right but also enhances the activity of other cell- and
signal-specific transcription factors.
NF-kB is activated by numerous extracellular
stimuli, including cytokines such as tumor necrosis
factor (TNF)-a and interleukin (IL)-1b, viruses, some
bacteria, and allergens. Activation of cell-surface re-
ceptors leads to phosphorylation of receptor-associ-
ated kinases, which in turn phosphorylate the
inhibitors of NF-kB kinase (IKKs). Phosphorylation
of IKKs results in phosphorylation of the NF-kB
cytoplasmic inhibitor (IkBa), so that IkBa is targe-
ted for proteosomal degradation. This degradation
TRANSCRIPTION FACTORS / Overview 247
precipitates the release of NF-kB from its inactive
state, enabling nuclear translocation and binding to
specific DNA response elements within the regula-
tory regions of responsive genes.
NF-kB is predominantly composed of the p50/p65
heterodimer. Changes in p65 phosphorylation status
can affect NF-kB function, for example, inactive p65
is nonphosphorylated and is associated predomi-
nantly with the repressor protein histone deace-
tylases 1 (HDAC1), whereas p65 is phosphorylated
following IKK-2 stimulation and is able to bind to
coactivator molecules such as CREB-binding protein
(CBP) and the related 300 kDa protein p300 (p300/
CBP). Acetylation of p65 may also influence NF-kB
function by affecting IkBa:p65 association and en-
hancing NF-kB activity.
Chromatin Modifications and Gene Expression
DNA is tightly compacted around a protein core to
form nucleosomes, which are further compacted to
form chromatin. Each individual nucleosome con-
sists of B146 bp DNA associated with an octamer of
two molecules each of core histone proteins (H2A,
H2B, H3, and H4). Since the early 1960s, it has
been known that the expression and repression of
genes is associated with alterations in chromatin
structure by enzymatic modification of core histones.
In the resting cell, DNA is tightly compacted around
these basic core histones, excluding the binding of
the enzyme RNA polymerase II, which activates the
formation of mRNA. This conformation of the chro-
matin structure is described as closed and is associ-
ated with suppression of gene expression (Figure 2).
The irregular 30 nm chromatin fiber is stabilized
and further compacted by interactions between nuc-
leosomes and linker histones such as H1. Histone H1
has long been regarded as a general repressor of
transcription, but there are indications that it also
has a role in transcriptional regulation. Here, histone
RNA
polymerase II
X
30 nm
chromatin
fiber
Figure 2 In the resting cell, DNA (gray bands) is tightly com-
pacted around core histones to form nucleosomes. These nuc-
leosomes are further compacted to form a closed inaccessible
structure, excluding the binding of the enzyme RNA polymerase
II, which activates the formation of messenger RNA. This chro-
matin structure is associated with a lack of gene expression.
248 TRANSCRIPTION FACTORS / Overview
H1 acts as a ‘gate’ to nucleosomal DNA, preventing
transcription factor DNA binding. Histone H1 re-
moval is needed for opening factors to bind, thus
making nucleosomal DNA accessible to further tran-
scription factor binding and transcription. Phosphor-
ylation of histone H1 may play an essential role in
activation of gene transcription.
Specific residues (lysines, arginines, and serines)
within the N-terminal tails are capable of being
posttranslationally modified by acetylation, methyl-
ation, ubiquitination, or phosphorylation, all of
which have been implicated in the regulation of gene
expression. Acetylation of the s-group on lysines re-
duces the charge of the histone residue and subse-
quently releases the tightly wound DNA, allowing the
recruitment of further large protein complexes. A
breakthrough in the discovery of the role of histone
acetylation was the demonstration that transcrip-
tional coactivators such as CBP and p300/CBP-
associated factor (pCAF) have intrinsic histone
acetyltransferase (HAT) activity, which is activated
by the binding of transcription factors such as NF-kB.
Increased gene transcription is therefore associated
with an increase in histone acetylation, whereas
hypoacetylation is correlated with reduced transcrip-
tion or gene silencing. Histone acetylation is an ac-
tive process whereby small changes in the activity of
HATs or histone deacetylases (HDACs) can mark-
edly affect the overall histone acetylase activity as-
sociated with inflammatory genes. Importantly, these
changes in histone acetylation appear to be targeted
toward regions of DNA associated with specific ac-
tivator sites within the regulatory regions of induced
inflammatory genes, although a global loosening of
histone structure has also been proposed. Under rest-
ing conditions, less than half of the potential lysine
residues available for acetylation are in fact acety-
lated, and these residues have a rapid turnover. This
situation suggests that even small changes above or
below the resting level are enough to lead to an ac-
tivated chromatin state. This model predicts that
changes in the ‘histone code’, the diverse range of
histone tail posttranslational modifications such
as acetylation, methylation, phosphorylation, and
ubiquitination that are set and maintained by his-
tone-modifying enzymes, must be translated into
downstream events extremely rapidly.
NF-jB Activation Induces Histone Acetylation
NF-kB can induce acetylation on both histone H3
and H4 in both a time- and concentration-dependent
manner depending upon the stimulus and the cell
type involved following the recruitment of a large
coactivator complex that contains the HAT proteins
CBP, p300/CBP-associated factor (pCAF), and trans-
criptional intermediary factor-2 (TIF-2). IL-1b can
also activate other pathways distinct from NF-kB
that can impinge on NF-kB activation. These
additional pathways, such as protein kinase C and
nonreceptor tyrosine kinases, may enhance NF-kB
activity, either by phosphorylating p65 and thereby
enhancing cofactor recruitment or by phosphoryla-
ting NF-kB-associated cofactors.
Temporal Association of NF-jB with DNA,
Cofactors, and Gene Induction
The simplistic model described above does not ex-
plain all aspects of NF-kB action, however. Immedi-
ate early genes such as IkBa do indeed bind NF-kB
to their promoters rapidly after lipopolysaccharide
(LPS) stimulation, but within 10 min NF-kB dissoci-
ates from the IkBa promoter site and never reasso-
ciates. In contrast, NF-kB binds to its promoter sites
in DNA for up to 2 h before dissociation in distinct
sets of genes (such as manganese superoxide di-
smutase and macrophage inflammatory protein-2), in
spite of stimulation by LPS at the same time. How-
ever, other NF-kB-regulated genes, such as the
chemokines/cytokines RANTES (regulated on acti-
vation, normal T cell expressed and % secreted), mon-
%
% % % %
ocyte chemoattractant protein-1, and IL-6, do not
show NF-kB binding to their promoters until 2 h af-
ter activation. NF-kB sites in the promoter regions of
these genes are originally in a repressed chromatin
environment that prevents NF-kB DNA binding and
subsequent gene expression. These become accessible
only after AP-1-mediated histone acetylation and
subsequent alteration in the local nucleosomal struc-
ture (chromatin remodeling) (Figure 3). Thus, there
are subtle changes in NF-kB DNA binding that are
promoter context-dependent, precede coactivator re-
cruitment, and are not detectable using conventional
band shift and reporter gene assays. The question as
to which aspect of chromatin changes occurs first,
remodeling or modification, prior to gene induction
is still a matter of intense debate.
The question arises: how can NF-kB, or any other
transcription factor, interact with its recognition site
when DNA is compacted? NF-kB may bind to a kB-
RE within the linker DNA between nucleosomes
or, alternatively, when the kB-RE core residues are
facing outward from the DNA wrapped around hi-
stones. Binding to the kB-RE may then modify the
local chromatin structure or cause local histone
modifications altering NF-kB access to the promoter
site. High-resolution mapping of GR interactions
with a glucocorticoid-responsive promoter suggests
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
have effects elsewhere, thereby enforcing a particular
translational frame on the chromatin template and
modifying the effects of other DNA-binding proteins.
Ordered Recruitment of Coactivator Complexes
One other important question that also needs to be
addressed is whether there is a specific order of re-
cruitment of distinct coactivator factors to the acti-
vated DNA-bound NF-kB complex to enable gene
transcription. Recent work examining androgen and
thyroid hormone receptor gene activation shows that
nuclear hormone receptors do not in themselves
recruit all the cofactors required at the target pro-
moters. Steroid receptor coactivators, recruited by
receptors, can in turn recruit other coactivators such
as p300/CBP, which can subsequently recruit SWI/
SNF (a large multisubunit protein complex) and
mediator complexes. SWI/SNF enables chromatin
remodeling to occur in an adenosine triphosphate
(ATP)-dependent manner, but histone acetylation by
p300/CBP facilitates the recruitment of SWI/SNF and
mediator complexes. Thus, cofactor–cofactor inter-
actions are essential for effective gene expression.
The interactions do not have to occur sequentially,
but histone acetylation can enhance the recruitment
of large multiprotein complexes in a coordinated
manner.
However, again the story is found to be more
complex. In some cases, such as the GR and possibly
p65, there is a ‘hit-and-run’ mechanism of action
rather than a stable association with glucocorticoid
response element (GRE). GR resides on DNA for less
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-
scription, such as HAT-containing complexes, and
may also play a role in feedback regulation. Inter-
estingly, in the absence of ATP and chromatin
remodeling factors, the GR stably interacts with
glucocorticoid-responsive genes.
Cross-Talk between Transcription
Factors and Their Transduction Pathways
The complexity of transcription factor activation
pathways and their ability to engage in cross-talk
may enable cells to overcome inhibition of one path-
way and retain a capacity to activate specific inflam-
matory genes. Generally, it is necessary to have
coordinate activation of several transcription factors
in order to have maximal gene expression. This may
explain how ubiquitous transcription factors may
regulate specific genes in certain types of cells only.
Activation of NF-kB leads to the coordinated induc-
tion of multiple inflammatory and immune genes.
Whilst NF-kB is not the only transcription factor in-
volved in regulation of these genes, it often appears
to have a decisive role often in cooperation with
other transcription factors such as AP-1 and C/EBP.
The role of NF-kB should be seen as an amplifying
250 TRANSCRIPTION FACTORS / Overview
and perpetuating mechanism that will exaggerate
the disease-specific inflammatory process through the
coordinated activation of multiple inflammatory
genes.
The fact that many inflammatory genes, which
are regulated by AP-1, NF-kB, and C/EBP, can be
downregulated by glucocorticoids indicates the pos-
sible importance of cross-talk between these signal
transduction pathways. For example, activation of
the IL-8 promoter by NF-kB and C/EBP is inhibited
by dexamethasone primarily via the NF-kB site.
Conversely, activation of a GRE-dependent promoter
by dexamethasone was inhibited by overexpression
of p65. These and other studies show direct protein–
protein interactions between NF-kB and GR, which
prevent NF-kB transactivation and partly account for
the anti-inflammatory properties of glucocorticoids.
GR represses AP-1 transactivation using mechanisms
similar to those used to inhibit NF-kB activation.
Transcription Factors in Lung Disease
There has been a recent increase in the number of
investigations of transcription factor activity and/or
expression in human respiratory diseases to provide
proof of concept and validation for murine disease
models. Many transcription factors such as p53,
TTF-1, early growth response-1 (Egr-1), STAT3, in-
sulin-derived growth factor (IGF), and RARs are in-
volved in the pathogenesis of lung carcinoma. In
addition, NF-kB also appears to play a critical role in
resistance to chemotherapy, inhibition of tumorigen-
esis, and the induction of anti-apoptotic genes.
NF-kB has been implicated in most, if not all, in-
flammatory diseases and diseases of the lung are no
exception. For example, NF-kB activity is enhanced
in asthma, chronic obstructive pulmonary disease
(COPD), cystic fibrosis, and mineral dust diseases. It
has been suggested that cystic fibrosis transmem-
brane regulator (CFTR) acts as a pattern recognition
receptor regulating NF-kB activity and the D508
mutation leads to constitutive NF-kB activation.
Furthermore, hepatic nuclear factor (HNF)-1 confers
tissue-selective expression of CFTR.
In addition, there is evidence for increased expres-
sion of c-Fos in bronchial epithelial cells in asthmatic
airways, and many of the stimuli relevant to asthma
that activate NF-kB will also activate AP-1. In ad-
dition, enhanced activity of both NF-kB and AP-1
has been reported in the airways of severe therapy-
insensitive asthmatic patients. In addition, a recent
study showed a genetic association of asthma sever-
ity with the zinc finger transcription factor PHF11.
Two transcription factors GATA-3 and T-bet
appear to be critically important for Th2 and Th1
polarization, respectively, by acting both on regu-
lated gene expression and by epigenetic control. For
example, GATA-3 seems to be of particular impor-
tance in the differentiation of human Th2 cells and
also the suppression of Th1 cytokine production by
resetting the Th1 and Th2 gene loci. T-bet performs a
similar function for Th1 differentiation and cytokine
production. GATA-3 expression is increased in the
peripheral venous blood T cells from atopic asth-
matics and in induced sputum cells from asthmatic
subjects particularly after allergen challenge and
T-bet appears to be overexpressed in Th1 diseases.
Understanding of the molecular mechanisms for
Th1 and Th2 cytokine production developed in an-
imal models predicts that altered expression of
STAT4 and STAT6 would be found in allergic air-
way disease. Despite convincing data in disease mod-
els, this has not been confirmed in man. Interestingly,
enhanced activation of STAT1 has been reported in
the airways of patients with asthma and in subjects
with cystic fibrosis. Protein inhibitor of activated
STAT1 (PIAS1) has also been implicated as playing a
role in the pathogenesis of cystic fibrosis. Sp1 is a
ubiquitous transcription factor that binds to GC-
boxes and related motifs, which are frequently oc-
curring DNA elements present in many promoters
and enhancers. Modification of these sites within the
IL-4, IL-10, and 5-lipoxygenase promoters has been
associated with altered expression of these genes in
distinct groups of asthmatic patients.
The expression of the GR has been examined in
several steroid-sensitive and -insensitive respiratory
diseases. GRa expression has been reported to be
lower in steroid-insensitive interstitial pulmonary fi-
brosis (IPF) than in steroid-sensitive diseases such as
sarcoidosis and cryptogenic organizing pneumonia
(COP). In contrast, no changes in GRa expression
have been reported in severe therapy-insensitive
asthma and determination of GRa expression in
COPD has not yet been reported. Changes in the
expression of GRb, a dominant negative form of GR,
do not appear to correlate with steroid sensitivity in
most lung diseases although this remains controver-
sial for severe asthma. Furthermore, abnormal
expression of other nuclear hormone receptors in-
cluding peroxisome proliferating antigen receptor
(PPAR)g and the vitamin D3 receptor (VD3R) has
been reported in BAL macrophages and T cells in
patients with sarcoidosis. Importantly, recent evi-
dence suggests that a dysfunctional interaction be-
tween GR and C/EBPa in airway smooth muscle cells
plays a role in their increased proliferation seen in
the lower airways of asthmatics and might explain
why this is not affected by treatment with inhaled
corticosteroids.

There is also evidence for activation of NF-kB in
the bronchial epithelial cells of patients with COPD
and in the sputum macrophages during COPD ex-
acerbations. Finally, there is an increased number of
activated STAT4þ cells in the bronchial biopsies of
smokers with mild–moderate COPD compared with
smokers with normal lung function. The presence of
activated STAT4þ cells is significantly associated
with the presence of IFN-gþ cells in both bronchial
biopsies and bronchoalveolar lavage-derived lympho-
cytes and correlates with the degree of airflow limi-
tation in smokers.
Transforming growth factor beta (TGF-b) is pos-
tulated to play a major role in several lung diseases
where airway remodeling has been implicated, such
as asthma, COPD, and fibrosing lung disease. TGF-b
stimulates a family of transcription factors known
as Smads. The Smad family consists of the receptor-
regulated Smads (R-Smads), a common pathway
Smad (co-Smad), and inhibitory Smads (anti-Smads).
R-Smads include Smads 1, 2, 3, 5, 8, and 9 and are
phosphorylated following TGF-b receptor binding.
Smad4 is a co-Smad and is not phosphorylated by the
TGF-b receptor binding. Anti-Smads include Smad6
and Smad7, which downregulate TGF-b receptor
signaling. Recent reports suggest that the expression
of the inhibitory SMADs 6 and 7 are significantly
downregulated in COPD. In addition, abnormal
Smad3 expression has been reported in pulmonary
hypertension and cystic fibrosis. Fibrosis has also
been associated with changes in hypoxia and specifi-
cally hypoxia-inducible factor (HIF)-1 and more
general redox-sensitive transcription factors such as
NF-kB and AP-1. Data from animal models have also
implicated a role for factors such as Thy1 and NRF2,
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.
Studies of transcription factor interactions may
thus have therapeutic potential in the control of
many lung diseases. Glucocorticoids are the most
effective treatment for asthma and exert their
anti-inflammatory effects largely by binding to trans-
cription factors that have been activated by inflam-
matory cytokines. Other drugs that regulate the
activity of specific transcription factors may also be
developed in the future. The identification of enzyme
targets, such as Jun kinases or IKKs, may also lead to
the development of new drugs that are able to con-
trol oncogenesis and/or inflammation. Cell-specific
transcription factors may be a more attractive target,
as this may lead to the development of drugs with a
reduced risk of adverse effects.
TRANSCRIPTION FACTORS / AP-1 251
See also: Corticosteroids: Glucocorticoid Receptors.
Transcription Factors: AP-1; ATF; Fox; NF-kB and Ikb;
POU; PU.1.
Further Reading
Andersen B and Rosenfeld MG (2001) POU domain factors in the
neuroendocrine system: lessons from developmental biology
provide insights into human disease. Endocrinology Review 22:
2–35.
Barnes PJ and Adcock IM (2003) How do corticosteroids work in
asthma? Annals of Internal Medicine 139: 359–370.
Caramori G, Ito K, and Adcock IM (2004) Transcription factors in
asthma and COPD. I Drugs 7: 764–770.
Escoubet-Lozach L, Glass CK, and Wasserman SI (2002) The role
of transcription factors in allergic inflammation. Journal of
Allergy and Clinical Immunology 110: 553–564.
Ghosh S and Karin M (2002) Missing pieces in the NF-kappaB
puzzle. Cell 109(supplement): S81–S96.
Groneberg DA, Witt H, Adcock IM, Hansen G, and Springer J
(2004) Smads as intracellular mediators of airway inflammation.
Experimental Lung Research 30: 223–250.
Hermanson O, Glass CK, and Rosenfeld MG (2002) Nuclear re-
ceptor coregulators: multiple modes of modification. Trends in
Endocrinology and Metabolism 13: 55–60.
Latchman DS (1999) Eukaryotic Transcription Factors, 3rd edn.
Oxford: Academic Press.
Pabo CO and Sauer RT (1992) Transcription factors: structural
families and principles of DNA recognition. Annual Review of
Biochemistry 61: 1053–1095.
Sharrocks AD (2001) The ETS-domain transcription factor family.
Nature Review of Cellular and Molecular Biology 2: 827–837.
Sirulnik A, Melnick A, Zelent A, and Licht JD (2003) Molecular
pathogenesis of acute promyelocytic leukaemia and APL vari-
ants. Best Practice and Research in Clinical Haematology 16:
387–408.
Urnov FD and Wolffe AP (2001) Chromatin remodeling and tran-
scriptional activation: the cast (in order of appearance). Onco-
gene 20: 2991–3006.
White RJ (2001) Gene Transcription: Mechanisms and Control.
Oxford: Blackwell.
AP-1
E Shaulian, Hebrew University Medical School,
Jerusalem, Israel
& 2006 Elsevier Ltd. All rights reserved.
Abstract
The AP-1 transcription factor is a dimeric transcription factor
composed of proteins from several families including Jun,
Fos, ATF, and Maf. AP-1 regulates various cell-autonomous as
well as general physiological and pathological effects. This
review describes the proteins making up AP-1, briefly mentions
the diverse mechanisms by which the expression and activity
of its components are regulated, and categorizes the major
types of genes regulated by it. The experimental evidence impli-
cating AP-1 in different processes such as proliferation, differ-
entiation, apoptosis, migration and wound healing, malignant