Basal Transcription Factors

The basal transcription factors are typically defined as the minimal complement of proteins
necessary to reconstitute accurate transcription from a minimal promoter (such as a TATA
element or initiator sequence). They are distinct from the regulatory transcription factors,
which bind to sequences farther away from the initiation site and serve to modulate levels of
transcription. This regulation presumably occurs through interactions between the regulatory
and basal transcription factors, although there is a great deal of controversy about the identity
of the regulatory factors' "target(s)"

The basal transcription complex assembles through an extensive series of protein-protein

interactions. Although the basal factors can assemble on the promoter in a step-wise manner
in vitro, there is some evidence that many of the factor interactions can occur in the absence
of DNA and that some of the factors may pre-assemble into a "holoenzyme".

The TATA binding protein (TBP) is a transcription factor that binds specifically to a DNA
sequence called the TATA box. This DNA sequence is found about 35 base pairs upstream of
the transcription start site in some eukaryotic gene promoters.[1] TBP, along with a variety of
TBP-associated factors, make up the TFIID, a general transcription factor that in turn makes
up part of the RNA polymerase II preinitiation complex.[2] As one of the few proteins in the
preinitiation complex that binds DNA in a sequence-specific manner, it helps position RNA
polymerase II over the transcription start site of the gene. However, it is estimated that only
10-20% of human promoters have TATA boxes. Therefore, TBP is probably not the only
protein involved in positioning RNA polymerase II.

TBP is involved in DNA melting (double strand separation) by bending the DNA by 80° (the
AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in
that it binds the minor groove using a β sheet.

Another distinctive feature of TBP is a long string of glutamines in the N-terminus of the
protein. This region modulates the DNA binding activity of the C-terminus, and modulation
of DNA binding affects the rate of transcription complex formation and initiation of
transcription. Mutations that expand the number of CAG repeats encoding this polyglutamine
tract, and thus increase the length of the polyglutamine string, are associated with
spinocerebellar ataxia 17, a neurodegenerative disorder classified as a polyglutamine disease.
[3]

Role as Transcription Factor Subunit

TBP is a subunit of the eukaryotic transcription factor TFIID. TFIID is the first protein to
bind to DNA during the formation of the pre-initiation transcription complex of RNA
polymerase II (RNA Pol II). Binding of TFIID to the TATA box in the promoter region of
the gene initiates the recruitment of other factors required for RNA Pol II to begin
transcription. Some of the other recruited transcription factors include TFIIA, TFIIB and
TFIIF. Each of these transcription factors are formed from the interaction of many protein
subunits, indicating that transcription is a heavily regulated process.

TBP is also a necessary component of RNA polymerase I and RNA polymerase III, and is
perhaps the only common subunit required by all three of the RNA polymerases
When TBP binds to a TATA box within the DNA, it distorts the DNA by inserting amino
acid side chains between base pairs, partially unwinding the helix, and doubly kinking it. The
distortion is accomplished through a great amount of surface contact between the protein and
DNA. TBP binds with the negatively charged phosphates in the DNA backbone through
positively charged lysine and arginine amino acid residues. The sharp bend in the DNA is
produced through projection of four bulky phenylalanine residues into the minor groove. As
the DNA bends, its contact with TBP increases, thus enhancing the DNA-protein interaction.

The strain imposed on the DNA through this interaction initiates melting, or separation, of the
strands. Because this region of DNA is rich in adenine and thymine residues, which base pair
through only two hydrogen bonds, the DNA strands are more easily separated. Separation of
the two strands exposes the bases and allows RNA polymerase II to begin transcription of the
gene.

TBP's C-terminus composes of a helicoidal shape that (incompletely) compliments the T-A-
T-A region of DNA. Interestingly this incompleteness allows DNA to be passively bent on
binding.

For information on the use of TBP in cells see: RNA polymerase I, RNA polymerase II and
RNA polymerase III

TFIIA
Composition: TFIIA consists of two subunits in yeast and three in humans and drosophila
(although two subunits are derived from a precursor protein).

Interactions: TFIIA binds directly to TBP and stabilizes its binding to DNA, perhaps through
direct contacts of its own with the DNA. TFIIA binding does not preclude TFIIB binding or
other components of the transcription complex. However, binding of TFIIA to TBP is
mutually exclusive with binding of some negative regulatory proteins.

Features: Both subunits of TFIIA are extremely acidic.

Functions: The current wisdom is that TFIIA acts as an anti-repressor, stabilizing TFIID
binding by blocking repressors of transcription that inhibit binding of other
transcription factors or that remove TBP from the DNA. Activation of transcription
may be dependent on this TFIIA functionTranscription factor TFIIA is a nuclear
protein involved in the RNA polymerase II-dependent transcription of DNA.[1]
TFIIA is one of several general (basal) transcription factors (GTFs) that are required
for all transcription events that use RNA polymerase II. Other GTFs include TFIID, a
complex composed of the TATA binding protein TBP and TBP-associated factors
(TAFs), as well as the factors TFIIB, TFIIE, TFIIF, and TFIIH. Together, these
factors are responsible for promoter recognition and the formation of a transcription
preinitiation complex (PIC) capable of initiating RNA synthesis from a DNA
templateFunctions

TFIIA interacts with the TBP subunit of TFIID and aids in the binding of TBP to TATA-box
containing promoter DNA. Although TFIIA does not recognize DNA itself, its interactions
with TBP allow it to stabilize and facilitate formation of the PIC. Binding of TFIIA to TBP
also results in the exclusion of negative (repressive) factors that might otherwise bind to TBP
and interfere with PIC formation. TFIIA also acts as a coactivator for some transcriptional
activators, assisting with their ability to increase, or activate, transcription. The requirement
for TFIIA in vitro transcription systems has been variable, and it can be considered either as a
GTF and/or a loosely associated TAF-like coactivator. Genetic analysis in yeast has shown
that TFIIA is essential for viability

TFIIA genes

TFIIA is encoded by two separate genes, one of which encodes a large subunit
(TFIIAalpha/beta, TFIIAL, TOA1; gene name GTF2A1)[2] and another which encodes a small
subunit (TFIIAgamma, TFIIAS, TOA2; gene name GTF2A2).[3] In humans, the sizes of the
encoded proteins are approximately 55 kD and 12 kD. Both genes are present in species
ranging from humans to yeast, and their protein products interact to form a complex
composed of a beta barrel domain and an alpha helical bundle domain. It is the N-terminal
and C-terminal regions of the large subunit that participate in interactions with the small
subunit. These regions are separated by another domain whose sequence is always present in
large subunits from various species but whose size varies and whose sequence is poorly
conserved. The large subunit is often observed to be proteolytically processed into two
smaller subunits (alpha and beta) of approximately 35 kD and 19 kD. A second gene
encoding a large TFIIA subunit has been found in some higher eukaryotes. This gene,
ALF/TFIIAtau (gene name GTF2A1LF) is expressed only in oocytes and spermatocytes,
suggesting it has a TFIIA-like regulatory role for gene expression only in germ cells

TFIIB

Protein composition: Single subunit. To date, all TFIIB proteins are between 35 and 40
kilodaltons.

Features: A zinc finger domain at the N-terminus and a direct repeat in a proteolytically
stable C-terminal domain.

Interactions: Binds directly to TBP, recruits RNA polymerase II, in part through an
interaction with the small subunit of TFIIF. Several acidic activators can bind TFIIB in vitro.

Functions: Stabilizes TBP binding to TATA element. Required for association of RNA
polymerase II to the initiation complex. May be a target for regulatory transcription factors.

TFIID

Composition: TFIID is a multi-component (>5 subunits) transcription factor that recognizes

and binds to the promoter DNA. TFIID consists of a DNA binding subunit that recognizes
the TATA element and is therefore designated TATA-binding protein (or TBP), as well as
several TBP-associated factors (or TAFs).

Interactions: TFIID acts to nucleate the transcription complex, recruiting the rest of the
factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for
TATA element binding and TFIIB interaction, and can support basal transcription. However,
this basal transcription reaction does not respond to upstream transcription activators. Many
of these regulatory factors interact with TBP or TAFs in various in vitro assays. TBP also
interacts directly with TFIIA.

Features: TBP consists of a 180 amino acid domain that is sufficient for activity. This domain
is made up of an imperfectly repeated sequence, and the repeats are reflected in the symmetry
of the molecule (see picture below). The protein resembles a saddle, with the inner surface
contacting DNA and the outer surface presumable making protein-protein contacts.

Functions: TFIID binding is thought to be the first step in transcription initiation. Some of the
TAFs also bind to initiator elements. TBP is also a component of the RNA polymerase I and
RNA polymerase III transcription complexes.

Transcription factor II D

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RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited

to the promoters of protein-coding genes in living cells. It consists of RNA polymerase II, a
subset of general transcription factors, and regulatory proteins known as SRB proteins.
Transcription factor II D (TFIID) is one of several general transcription factors that make up
the RNA polymerase II preinitiation complex.[1] Before the start of transcription, the
transcription Factor II D (TFIID) complex, consisting of TFIID, TBP, and at least nine other
polypeptides, binds to the TATA box in the core promoter of the gene.

TFIID is itself composed of several subunits called TBP-associated factors (TAFs, of which
there are 16) and the TATA Binding Protein (TBP). In a test tube, only TBP is necessary for
transcription at promoters that contain a TATA box.[2] TAFs, however, add promoter
selectivity, especially if there is no TATA box sequence for TBP to bind to. TAFs are
included in two distinct complexes, TFIID and B-TFIID.[3] The TFIID complex is composed
of TBP and more than eight TAFs. But, the majority of TBP is present in the B-TFIID
complex, which is composed of TBP and TAFII170 (BTAF1) in a 1:1 ratio.[4]

TFIID (GTF2D)

1. coordinates the activities of more than 70 polypeptides required for iniation of

transcription by RNA polymerase II,
2. binds to the core promoter to position the polymerase properly,
3. serves as the scaffold for assembly of the remainder of the transcription complex, and
4. acts as a channel for regulatory signals
TFIIE

Composition: Two subunits. Probably a tetramer consisting of two molecules of each subunit.

Features: Large subunit has a zinc finger domain.

Interactions: TFIIE modulates the helicase and kinase activities of TFIIH and the two factors
show species-specific interactions.

Functions: Recruits TFIIH to the initiation complex and modulates TFIIH kinase and helicase
activities. Appears to be required for escape of the RNA polymerase into elongation mode
(promoter clearance

TFIIF

Composition: Two subunits (yeast has a third non-essential protein associated).

Features:

Interactions: TFIIF binds directly to RNA polymerase II (and was originally isolated as an
RNA polymerase II associated protein or RAP). TFIIF is necessary for RNA polymerase II to
stably associate with the TFIIF-TFIIB-promoter complex. There is a protein interaction
between the small subunit and TFIIB in vitro and a genetic interaction between the large
subunit and TFIIB.

Functions: Helps recruit RNA polymerase II to the initiation complex in collaboration with
TFIIB. TFIIF is a component of the yeast holoenzyme and mediator complexes. Promotes
transcription elongation, may remain associated with the elongating polymerase.

TFIIH

Composition: Mammalian and yeast TFIIHs have at least six subunits. Most subunits are now
cloned, although not all are published.

Yeast subunits: SSL2(RAD25), RAD3, SSL1, TFB1, TFB2, TFB3, TFB4.

In addition to the TFIIH subunits, there is an associated complex consisting of a CDC-like

kinase and cyclin-like subunit. This kinase complex is sometimes referred to as TFIIK. Yeast
subunits: KIN28 and CCL1.

Features: The two largest TFIIH subunits are ATP-dependent helicases of opposite polarity.
Two of the smaller subunits have possible zinc finger domains.

Interactions: TFIIH appears to be dependent upon TFIIE for incorporation into the initiation
complex. The associated kinase (TFIIK) complex can phosphorylate the C-terminal domain
of the pol II largest subunit.
Functions: TFIIH is essential for promoter melting (separation of the two DNA strands)
and/or promoter clearance (i.e. for pol II to break free of the initiation complex into
elongation mode). Surprisingly, TFIIH also is essential for Nucleotide Excision Repair
(NER) of damaged DNA. The relationship between TFIIH's transcription and repair functions
is not understood yet.

Transcription factor II H (TFIIH) is one of several general transcription factors that make up
the RNA polymerase II preinitiation complex. TFIIH consists of ten subunits, 7 of which
(XPD, XPB, p62, p52, p44, p34 and TTDA) form the core complex. The cyclin activating
kinase-subcomplex (CDK7, MAT1, and cyclin H) is linked to the core via the XPD protein [1]
Two of the subunits, ERCC2/XPD and ERCC3/XPB, have helicase and ATPase activities
and help create the transcription bubble. In a test tube these subunits are only required for
transcription if the DNA template is not already denatured or if it is supercoiled. Two other
TFIIH subunits, CDK7 and cyclin H, phosphorylate serine amino acids on the RNA
polymerase II C-terminal domain and possibly other proteins involved in the cell cycle. Next
to a vital function in transcription initiation, TFIIH is also involved in nucleotide excision
repair.

Transcription factor

From Wikipedia, the free encyclopedia

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In the field of molecular biology, a transcription factor (sometimes called a sequence-specific

DNA binding factor) is a protein that binds to specific DNA sequences and thereby controls
the transfer (or transcription) of genetic information from DNA to mRNA.[1][2] Transcription
factors perform this function alone or with other proteins in a complex, by promoting (as an
activator), or blocking (as a repressor) the recruitment of RNA polymerase (the enzyme that
performs the transcription of genetic information from DNA to RNA) to specific genes.[3][4][5]

A defining feature of transcription factors is that they contain one or more DNA-binding
domains (DBDs), which attach to specific sequences of DNA adjacent to the genes that they
regulate.[6][7] Additional proteins such as coactivators, chromatin remodelers, histone
acetylases, deacetylases, kinases, and methylases, while also playing crucial roles in gene
regulation, lack DNA-binding domains, and therefore are not classified as transcription
factors

Conservation in different organisms

Transcription factors are essential for the regulation of gene expression and are, as a
consequence, found in all living organisms. The number of transcription factors found within
an organism increases with genome size, and larger genomes tend to have more transcription
factors per gene.[9]

There are approximately 2600 proteins in the human genome that contain DNA-binding
domains, and most of these are presumed to function as transcription factors.[10] Therefore,
approximately 10% of genes in the genome code for transcription factors, which makes this
family the single largest family of human proteins. Furthermore, genes are often flanked by
several binding sites for distinct transcription factors, and efficient expression of each of
these genes requires the cooperative action of several different transcription factors (see, for
example, hepatocyte nuclear factors). Hence, the combinatorial use of a subset of the
approximately 2000 human transcription factors easily accounts for the unique regulation of
each gene in the human genome during development.

Mechanism

Transcription factors bind to either enhancer or promoter regions of DNA adjacent to the
genes that they regulate. Depending on the transcription factor, the transcription of the
adjacent gene is either up- or down-regulated. Transcription factors use a variety of
mechanisms for the regulation of gene expression.[11] These mechanisms include:

• stabilize or block the binding of RNA polymerase to DNA

• catalyze the acetylation or deacetylation of histone proteins. The transcription factor
can either do this directly or recruit other proteins with this catalytic activity. More
specially many transcription factors use one or the other of two opposing mechanisms
to regulate transcription:[12]
o histone acetyltransferase (HAT) activity – acetylates histone proteins, which
weakens the association of DNA with histones, which make the DNA more
accessible to transcription and thereby upregulate transcription
o histone deacetylase (HDAC) activity – deacetylates histone proteins, which
strengthens the association of DNA with histones, which make the DNA less
accessible to transcription and thereby down regulate transcription
• recruit coactivator or corepressor proteins to the transcription factor DNA complex
• Function
•
•
• The transcription factor TATA binding protein (blue) bound to DNA (red). Image by
David S. Goodsell based on the crystal structure 1cdw from the Protein Data Bank.
• Transcription factors are one of the groups of proteins that read and interpret the
genetic "blueprint" in the DNA. They bind DNA and help initiate a program of
increased or decreased gene transcription. As such, they are vital for many important
cellular processes. Below are some of the important functions and biological roles
transcription factors are involved in:

Differential enhancement of transcription

Other transcription factors differentially regulate the expression of various genes by binding
to enhancer regions of DNA adjacent to regulated genes. These transcription factors are
critical to making sure that genes are expressed in the right cell at the right time and in the
right amount depending on the changing requirements of the organism.

[edit] Development

Many transcription factors in multicellular organisms are involved in development.[18]

Responding to cues (stimuli), these transcription factors turn on/off the transcription of the
appropriate genes, which, in turn, allows for changes in cell morphology or activities needed
for cell fate determination and cellular differentiation. The Hox transcription factor family,
for example, is important for proper body pattern formation in organisms as diverse as fruit
flies to humans.[19][20] Another example is the transcription factor encoded by the Sex-
determining Region Y (SRY) gene, which plays a major role in determining gender in
humans.[21]

[edit] Response to intercellular signals

Cells can communicate with each other by releasing molecules that produce signaling
cascades within another receptive cell. If the signal requires upregulation or downregulation
of genes in the recipient cell, often transcription factors will be downstream in the signaling
cascade.[22] Estrogen signaling is an example of a fairly short signaling cascade that involves
the estrogen receptor transcription factor: estrogen is secreted by tissues such as the ovaries
and placenta, crosses the cell membrane of the recipient cell, and is bound by the estrogen
receptor in the cell's cytoplasm. The estrogen receptor then goes to the cell's nucleus and
binds to its DNA-binding sites, changing the transcriptional regulation of the associated
genes.[23]

[edit] Response to environment

Not only do transcription factors act downstream of signaling cascades related to biological
stimuli but they can also be downstream of signaling cascades involved in environmental
stimuli. Examples include heat shock factor (HSF), which upregulates genes necessary for
survival at higher temperatures,[24] hypoxia inducible factor (HIF), which upregulates genes
necessary for cell survival in low-oxygen environments,[25] and sterol regulatory element
binding protein (SREBP), which helps maintain proper lipid levels in the cell.[26]

[edit] Cell cycle control

Many transcription factors, especially some that are oncogenes or tumor suppressors, help
regulate the cell cycle and as such determine how large a cell will get and when it can divide
into two daughter cells.[27][28] One example is the Myc oncogene, which has important roles in
cell growth and apoptosis.[29]

[edit] Regulation

It is common in biology for important processes to have multiple layers of regulation and
control. This is also true with transcription factors: not only do transcription factors control
the rates of transcription to regulate the amounts of gene products (RNA and protein)
available to the cell, but transcription factors themselves are regulated (often by other
transcription factors). Below is a brief synopsis of some of the ways that the activity of
transcription factors can be regulated:

[edit] Synthesis

Transcription factors (like all proteins) are transcribed from a gene on a chromosome into
RNA, and then the RNA is translated into protein. Any of these steps can be regulated to
affect the production (and thus activity) of a transcription factor. One interesting implication
of this is that transcription factors can regulate themselves. For example, in a negative
feedback loop, the transcription factor acts as its own repressor: if the transcription factor
protein binds the DNA of its own gene, it will down-regulate the production of more of itself.
This is one mechanism to maintain low levels of a transcription factor in a cell.

[edit] Nuclear localization

In eukaryotes, transcription factors (like most proteins) are transcribed in the nucleus but are
then translated in the cell's cytoplasm. Many proteins that are active in the nucleus contain
nuclear localization signals that direct them to the nucleus. But, for many transcription
factors, this is a key point in their regulation. [30] Important classes of transcription factors such
as some nuclear receptors must first bind a ligand while in the cytoplasm before they can
relocate to the nucleus.[30]

[edit] Activation

Transcription factors may be activated (or deactivated) through their signal-sensing domain
by a number of mechanisms including:

• ligand binding – Not only is ligand binding able to influence where a transcription
factor is located within a cell but ligand binding can also affect whether the
transcription factor is in an active state and capable of binding DNA or other cofactors
(see for example nuclear receptors).
• phosphorylation[31][32] – Many transcription factors such as STAT proteins must be
phosphorylated before they can bind DNA.
• interaction with other transcription factors (e.g., homo- or hetero-dimerization) or
coregulatory proteins

[edit] Accessibility of DNA-binding site

In eukaryotes, genes that are not being actively transcribed are often located in
heterochromatin. Heterochromatin are regions of chromosomes that are heavily compacted
by tightly bundling the DNA onto histones and then organizing the histones into compact
chromatin fibers. DNA within heterochromatin is inaccessible to many transcription factors.
For the transcription factor to bind to its DNA-binding site, the heterochromatin must first be
converted to euchromatin, usually via histone modifications. A transcription factor's DNA-
binding site may also be inaccessible if the site is already occupied by another transcription
factor. Pairs of transcription factors can play antagonistic roles (activator versus repressor) in
the regulation of the same gene.

[edit] Availability of other cofactors/transcription factors

Most transcription factors do not work alone. Often for gene transcription to occur, a number
of transcription factors must bind to DNA regulatory sequences. This collection of
transcription factors in turn recruit intermediary proteins such as cofactors that allow efficient
recruitment of the preinitiation complex and RNA polymerase. Thus, for a single
transcription factor to initiate transcription, all of these other proteins must also be present,
and the transcription factor must be in a state where it can bind to them if necessary.

[edit] Structure
Schematic diagram of the amino acid sequence (amino terminus to the left and carboxylic
acid terminus to the right) of a prototypical transcription factor that contains (1) a DNA-
binding domain (DBD), (2) signal sensing domain (SSD), and a transactivation domain
(TAD). The order of placement and the number of domains may differ in various types of
transcription factors. In addition, the transactivation and signal sensing functions are
frequently contained within the same domain.

Transcription factors are modular in structure and contain the following domains:[1]

• DNA-binding domain (DBD), which attach to specific sequences of DNA (enhancer

or promoter sequences) adjacent to regulated genes. DNA sequences that bind
transcription factors are often referred to as response elements.
• Trans-activating domain (TAD), which contain binding sites for other proteins such as
transcription coregulators. These binding sites are frequently referred to as activation
functions (AFs).[33]
• An optional signal sensing domain (SSD) (e.g., a ligand binding domain), which
senses external signals and in response transmit these signals to the rest of the
transcription complex, resulting in up or down regulation of gene expression. Also,
the DBD and signal-sensing domains may reside on separate proteins that associate
within the transcription complex to regulate gene expression.

[edit] Trans-activating domain

Trans-activating domains (TADs) are named after their amino acid composition. These amino
acids are either essential for the activity or simply the most abundant in the TAD.
Transactivation by the Gal4 transcription factor is mediated by acidic amino acids whereas
hydrophobic residues in Gcn4 play a similar role. Hence the TADs in Gal4 and Gcn4 are
referred to as acidic or hydrophobic activation domains respectively.[34]

Nine-amino-acid transactivation domain (9aaTAD) defines a novel domain common to a

large superfamily of eukaryotic transcription factors represented by Gal4, Oaf1, Leu3, Rtg3,
Pho4, Gln3, Gcn4 in yeast and by p53, NFAT, NF-κB and VP16 in mammals.[35] Prediction
for 9aa TADs (for both acidic and hydrophilic transactivation domains) is available online
from ExPASy [36] and EMBnet Spain [37]

9aaTAD transcription factors p53, VP16, MLL, E2A, HSF1, NF-IL6, NFAT1 and NF-kB
interact directly with the general coactivators TAF9 and CBP/p300.[38] p53 9aaTADs interact
with TAF9, GCN5 and with multiple domains of CBP/p300 (KIX, TAZ1,TAZ2 and IBiD).[39]

KIX domain of general coactivators Med15(Gal11) interacts with 9aaTAD transcription

factors Gal4, Pdr1, Oaf1, Gcn4, VP16, Pho4, Msn2, Ino2 and P201.[40] Interactions of Gal4,
Pdr1 and Gcn4 with Taf9 were reported. [41] 9aaTAD is a common transactivation domain
recruits multiple general coactivators TAF9, MED15, CBP/p300 and GCN5
Response elements

The DNA sequence that a transcription factor binds to is called a transcription factor-binding
site or response element.[50]

Transcription factors interact with their binding sites using a combination of electrostatic (of
which hydrogen bonds are a special case) and Van der Waals forces. Due to the nature of
these chemical interactions, most transcription factors bind DNA in a sequence specific
manner. However, not all bases in the transcription factor-binding site may actually interact
with the transcription factor. In addition, some of these interactions may be weaker than
others. Thus, transcription factors do not bind just one sequence but are capable of binding a
subset of closely related sequences, each with a different strength of interaction.

For example, although the consensus binding site for the TATA-binding protein (TBP) is
TATAAAA, the TBP transcription factor can also bind similar sequences such as TATATAT
or TATATAA.

Because transcription factors can bind a set of related sequences and these sequences tend to
be short, potential transcription factor binding sites can occur by chance if the DNA sequence
is long enough. It is unlikely, however, that a transcription factor binds all compatible
sequences in the genome of the cell. Other constraints, such as DNA accessibility in the cell
or availability of cofactors may also help dictate where a transcription factor will actually
bind. Thus, given the genome sequence it is still difficult to predict where a transcription
factor will actually bind in a living cell.

Additional recognition specificity, however, may be obtained through the use of more than
one DNA-binding domain (for example tandem DBDs in the same transcription factor or
through dimerization of two transcription factors) that bind to two or more adjacent
sequences of DNA.