The complex processes of eukaryotic gene

expression are controlled by a relatively

small number of transcription factors whose

activities are modulated by a diverse set of

regulatory mechanisms. A recent paper

describes the molecular basis for one such

mechanism in which the Pit-1 transcription

factor activates or represses transcription

depending on the sequence of the DNA to

which it binds. The mechanism by which the

binding-site sequence regulates the activity

of Pit-1 is discussed in relation to that of

other transcription factors.

Early studies of eukaryotic gene

regulation identified specific, short DNA

sequences that were present in all genes

activated by a common stimulus but

absent from genes that were not regulated

by this stimulus (reviewed in Ref. 1).

Subsequently, it was shown that these

sequences (e.g. the heat shock element or

the glucocorticoid response element) acted

by binding positively acting transcription

factors, which were activated by the

stimulus. The activation of these

transcription factors resulted in the

stimulation of gene transcription

(reviewed in Refs 2,3).

These early studies led to the idea that

transcription factors regulated gene

expression in a positive manner in response

to specific stimuli, or in particular cell types.

Subsequently, however, it became clear that

many transcription factors could act by

inhibiting, as opposed to activating, gene

expression. Such repression can occur either

via a negatively acting factor interfering

with the action of a positively acting factor,

or by a direct interaction between the

negative factor and the basal transcriptional

complex that reduces the activity of this

complex (reviewed in Refs 2,4). In turn,

these studies led to the idea that the

transcription rate of a particular gene, either

in a specific cell type or following exposure to

a particular stimulus, was regulated by the

relative balance of activating and inhibiting

transcription factors.

A single factor can both activate and

repress transcription

Although this idea is basically correct, the

situation has become more complex as

further studies have been conducted. In

particular, it is now becoming increasingly

recognized that although some factors are

pure activators or pure repressors, many

can both activate and repress transcription

in a manner that is dependent on the

particular situation.

Steroid and thyroid hormone receptorsAn early example of such a ‘dual’-acting

transcription factor was provided by the

thyroid hormone receptor, which regulates

gene expression in response to thyroid

hormone and is a member of the nuclear

receptor gene superfamily (i.e. the steroid

hormone receptor family) of transcription

factors (reviewed in Ref. 5). In the absence

of thyroid hormone, the thyroid hormone

receptor binds to its DNA-binding site in

thyroid hormone-responsive genes, albeit

in a conformation that enables it to bind

co-repressor molecules such as N-CoR and

mSIN3; consequently, transcription is

repressed (Fig. 1a). However, following

binding of thyroid hormone, the receptor

changes its conformation so that it can no

longer bind co-repressor molecules.

Instead, the receptor binds coactivator

molecules such as CREB binding protein

(CBP), resulting in the activation of

transcription (Fig. 1a).

In the case of the thyroid hormone

receptor, therefore, a single transcription

factor can act as either an activator or a

repressor depending on the presence or

absence of thyroid hormone, respectively.

Interestingly however, in the case of the

glucocorticoid receptor (another member of

the nuclear receptor family of transcription

factors), the ability of the receptor to

activate or repress transcription depends on

the nature of the DNA sequence to which it

is bound. Unlike the thyroid hormone

receptor, the glucocorticoid receptor binds to

its DNA target sites only following hormone

treatment. Initial studies focused on genes

that were activated by this steroid hormone

and that contained a glucocorticoid

response element (GRE). Following

hormone binding, the glucocorticoid

receptor binds as a dimer to the GRE and

activates transcription (Fig. 1b; reviewed in

Refs 6,7). However, subsequent studies

indicated that there were other genes

(e.g. that encoding proopiomelanocortin)

that are repressed by the glucocorticoid

receptor following hormone treatment and

that contain a sequence distinct from, but

related to, the GRE, known as an nGRE.

Interestingly, it has been demonstrated that

the receptor binds to this nGRE as a trimer

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211Research Update

Transcription factors: bound to activate or repress

David S. Latchman

GR No transcription

–

–GR

nGRE

GR

Transcription

GR GR+

GRE

No transcriptionTRE TRE

Transcription

+–TRTR

(a)

(b)

Ti BS

–T

GRE sequence nGRE sequence

+T

T

Fig. 1. Activation and repression by members of the nuclear receptor family: (a) In the absence of thyroid hormone (T),the thyroid hormone receptor (TR) binds to the thyroid hormone response element (TRE) in a conformation that binds co-repressor molecules and thereby inhibits transcription. Following binding of thyroid hormone, the structure of thereceptor changes so that it binds coactivator molecules and activates transcription. (b) The glucocorticoid receptor (GR)binds as a dimer to the glucocorticoid response element (GRE) and activates transcription. By contrast, the receptor bindsas a trimer to the related but distinct negative GRE (nGRE) sequence and represses rather than activates transcription.

rather than as a dimer (Fig.1b), and this

receptor trimer represses rather than

activates transcription8 (reviewed in Ref. 6).

Pit-1A recent paper by Scully et al.9 has

extended this idea to the cell type-specific

transcription factor Pit-1, demonstrating

the precise structural basis for the ability

of this factor to act as either an activator or

repressor of cell-type specific genes

depending on the nature of its binding site.

Pit-1 is a founding member of the POU

(Pit, Oct, Unc) family of transcription

factors, which play key roles in regulating

gene expression during development

(reviewed in Ref. 10). These proteins have

a bipartite DNA-binding domain

consisting of a POU-specific domain and a

POU-homeodomain related to the

homeobox found in other transcription

factors. Pit-1 plays a key role in

development of the pituitary gland and is

required for activation of the genes

encoding growth hormone, prolactin and

thyrotropin in somatotrope, lactotrope

and thyrotrope cell types, respectively. A

key question in understanding this system

is how Pit-1 activates only the appropriate

gene in each cell type.

The study by Scully et al.9 throws light

on this question. The authors focus their

attention on the fact that the binding site

for Pit-1 in the gene encoding growth

hormone, contains an extra two bases in

the centre of the site compared to the

Pit-1-binding site in the prolactin (PRL)

gene. They therefore prepared a construct

in which the Pit-1 binding site from the

growth hormone (GH1) promoter was

substituted with that from the PRL gene in

an otherwise intact GH1 promoter. When

this construct was introduced into

transgenic animals, the GH1 promoter was

expressed not only in somatotropes but also

in lactotropes, where normally only the

PRL promoter is active. Hence, in

lactotropes, Pit-1 can bind to its binding

sites in the PRL and GH1 promoters, and

activate or repress transcription of the

corresponding genes, respectively (Fig. 2a).

In further studies, Scully et al.9

cocrystallized Pit-1 with its two different

binding sites and showed that the

additional two-base pair sequence in the

growth hormone site results in the POU-

specific and POU-homeodomain portions

of the POU domain being accommodated

on the same face of the DNA, whereas on

the prolactin element, they are bound to

perpendicular faces of the DNA.

Hence, although both DNA sites bind a

Pit-1 dimer, this dimer is in distinct

conformations in the two situations. In

addition, Scully et al.9 were able to

demonstrate that, in lactotropes, the co-

repressor N-CoR is able to bind to the Pit-1

dimer that is bound to the promoter of the

GH1 gene, resulting in the repression of

expression. By contrast, this repressor

molecule does not bind to the Pit-1 dimer

bound to the prolactin-binding site and,

therefore, Pit-1 activates expression from

this promoter in lactotropes.

Although this study helps explain how

Pit-1 can selectively activate and/or

repress gene expression in a particular

cell type, it does not provide the complete

story because Pit-1 must also be able to

activate growth hormone expression in

the distinct somatotrope cell type. The

nature of the ‘override’mechanism by

which the repressive activity of Pit-1 on

the GH1 promoter is reversed in this cell

type, awaits further study. Nonetheless,

the work of Scully et al.9 advances our

understanding of the role of DNA

sequences in regulating the activity of

transcription factors.

Oct-1Interestingly, the POU family of

transcription factors to which Pit-1

belongs, has been subject to a variety of

different studies that have previously

elucidated the key role of DNA-binding

sites in other aspects of these factors. For

example, the Oct-1 transcription factor acts

as a weak transactivator, stimulating the

expression of several cellular genes that

contain its specific binding site

ATGCAAAT. However, following binding of

Oct-1 to the related sequence TAATGARAT

(R =purine) in the immediate-early gene

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212 Research Update

N-CoR

TATACATTTATTCATG

–Pit-1 Pit-1

ATGCATATGCATWeak transcription

Oct-1 Oct-1 +

ATGCAAAT

Weak transcription

Oct-1 +

ATTTGAAATGCAAAT

Strong transcription

+ +Oct-1 Oct-1

OBF-1 OBF-1

TATATATATTCATG

+

TAATGARAT

Strong transcription

+ +Oct-1

VP16

Pit-1 Pit-1

Prolactin Growth hormone

MORE sequence PORE sequence

Ti BS

HSV immediate-early genes

(a)

(c)

(b) Cellular genes

No transcription Transcription

Fig. 2. (a) Following binding to its DNA site in the promoter of the PRL gene, the Pit-1 dimer activates transcription. Bycontrast, the two extra T bases (shown in bold) in the centre of the binding site for Pit-1 in the GH1 promoter results in adifferent conformation following binding of transcription factor to DNA, which results in the recruitment of the N-CoRtranscriptional co-repressor and consequent transcriptional repression. (b) Binding of Oct-1 to the TAATGARAT sequencein the HSV immediate-early gene promoters results in a change in the conformation of this transcription factor, allowingit to bind the strong transcriptional activator VP16. Recruitment of VP16 does not occur upon binding of Oct-1 to theATGCAAAT sequence in cellular genes and, consequently, transcriptional activation is only weak. (c) Dimerization of Oct-1 on the MORE sequence results in the masking of the amino acid residues (red line) that are normally used to interactwith the transcriptional coactivator OBF-1 and hence only weak activation of transcription occurs. By contrast, followingdimerization on the PORE sequence, these amino acids are exposed and can be used to recruit OBF-1, leading to strongactivation of transcription. Abbreviations: GH1, gene encoding growth hormone; HSV, herpes simplex virus; MORE, morePORE; OBF–1, Oct-binding factor 1; PORE, palendromic Oct factor recognition element; PRL, gene encoding prolactin.

promoters of herpes simplex virus (HSV),

transcription is strongly activated. This

differential binding affinity results from a

conformational change in Oct-1, induced

upon binding to the TAATGARAT

sequence, that allows it to bind the HSV

VP16 (Vmw65) protein (a strong

transactivator), thereby increasing the

transactivation potency of Oct-1 (Ref. 11)

(Fig. 2b).

A recent study12 has extended this to

the binding of a cellular transcriptional

coactivator, OBF-1 (Oct-binding factor 1),

to dimers of Oct-1 that are bound to two

distinct sites with different sequences.

Thus, when Oct-1 binds as a dimer to a

sequence known as the palendromic Oct

factor recognition element (PORE), it

can then bind OBF-1, resulting in strong

activation of transcription. By contrast,

when Oct-1 binds as a dimer to the site

known as MORE (More PORE), the

residues in Oct-1 that interact with

OBF-1 on the PORE site are used

instead to form the dimer interface

between the Oct-1 monomers. Hence,

when bound to the MORE site, Oct-1

cannot recruit OBF-1, and strong

activation of transcription is precluded

(Fig. 2c).

Conclusion: the key role of the DNA-binding siteA variety of studies into transcriptional

regulation indicate that the DNA binding

site is not simply a passive partner that is

merely recognized by a particular

transcription factor. Rather, when

transcription factors bind to different sites

they assume different protein structures.

In turn, these structures determine

whether the bound transcription factor can

interact with particular coactivator or co-

repressor proteins. Hence, protein changes,

which occur on DNA binding, provide an

additional facet to the complexity of

transcription factors, allowing them to

activate transcription to varying degrees,

to have no effect, or to inhibit transcription.

This mechanism is one of many that enable

transcription factors to control the

inducible and cell type-specific gene

expression that is central to the

complexity of the multicellular eukaryotic

organism.

References

1 Latchman, D.S. (1998) Gene Regulation –

a eukaryotic perspective (3rd edn), Stanley Thorne

Publishers

2 Latchman, D.S. (1998) Eukaryotic transcription

factors (3rd edn), Academic Press

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213Research Update

Nicastrin, a protein implicated in

Alzheimer’s disease, has a domain that is

found in the aminopeptidase/transferrin

receptor superfamily. In nicastrin, this

domain might possess catalytic activity (as

observed with aminopeptidases) or it

could serve merely as a binding domain

(with analogy to the transferrin receptors)

for the ββ-amyloid precursor protein.

Nicastrin is a 709 amino acid type I

transmembrane glycoprotein that has been

recently identified1 as a key component of

the Alzheimer-linked multiprotein complex

formed with the proteases presenilin 1 and

presenilin 2. The formation of this complex

is the final step in the production of the

neurotoxic β-amyloid peptide (also known

as the amyloid), which is observed in brain

plaques of familial Alzheimer’s disease

patients. The amyloid protein is produced

from the membrane-bound β-amyloid

precursor protein, β-APP, in two distinct

sequential steps. First, β-APP is cleaved by

the protease β-secretase (BACE-2) and

second, the amyloid protein is liberated by

further γ-secretase processing. Current

opinion suggests that presenilin 1 and

presenilin 2 possess the protease catalytic

activity that is necessary for the production

of the neurotoxic β-amyloid peptide

(amyloid protein)1,2.

It was shown recently that nicastrin

binds to β-APP (and its α- and β-cleaved

versions) and is able to modulate the

production of β-amyloid peptide1. This

implicates a direct role for nicastrin in the

pathogenesis of Alzheimer’s disease and

suggests that it could be a suitable target

for therapeutic intervention. It was

speculated that the function of nicastrin

might be to bind substrates of

presenilin–γ-secretase complexes or,

alternatively, to modulate γ-secretase

activity. However, no significant amino

acid sequence similarity with known

proteases, nor indeed with any other

functionally annotated proteins, was

found. The molecular basis for biological

function of this protein therefore

remained unclear.

We show through the use of Genome

Threader (Ref. 3; Fig. 1) that the central

region of nicastrin is a new member of the

aminopeptidase superfamily, which also

includes the non-protease transferrin

receptor (TfR). Furthermore, these

Protein Sequence Motif

Nicastrin, a presenilin-interacting protein, contains an

aminopeptidase/transferrin receptor superfamily domain

Richard Fagan, Mark Swindells, John Overington and Malcolm Weir

3 Latchman, D.S., ed., (1997) Landmarks in Gene

Regulation, Portland Press

4 Hanna-Rose, W. and Hansen, U. (1996) Active

repression mechanisms of eukaryotic transcription

repressors. Trends Genet. 12, 229–234

5 Mangelsdorf, D.J. et al. (1995) The nuclear receptor

super family; the second decade. Cell 83, 835–839

6 Lefstin, J.A. and Yamamoto, K.R. (1998) Allosteric

effects of DNA on transcriptional regulators.

Nature 392, 885–888

7 Beato, M. et al. (1995) Steroid hormone receptors:

many actors in search of a plot. Cell 83, 851–857

8 Drouin, J. et al. (1993) Novel glucocorticoid receptor

complex with DNA element of the hormone

repressed POMC gene. EMBO J. 12, 145–156

9 Scully, K.M. et al. (2000) Allosteric effects of Pit-1

DNA sites on long-term repression in cell type

specification. Science 290, 1127–1131

10 Ryan, A.K. and Rosenfeld, M.G. (1997) POU

domain family values: flexibility, partnerships and

developmental codes. Genes Dev. 11, 1207–1225

11 Walker, S. et al. (1994) Site-specific

conformational alteration of the Oct-1 POU

domain–DNA complex as the basis for

differential recognition by Vmw65 (VP16). Cell

741, 841–852

12 Tomilin, A. et al. (2000) Synergism with the

coactivator OBF-1 (OCA-B, BOB-1) is mediated by a

specific POU dimer configuration. Cell103, 853–864

David S. Latchman

Institute of Child Health, University CollegeLondon, 30 Guilford Street, London, UKWC1N 1EH.e-mail: d.latchman@ich.ucl.ac.uk