Latchman. Eukariotic Transciption Factors

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the target genes to which they bind. This can result in factors with identical

DNA bindi ng specificities having entirely different functional effects as in the

case of Ubx and Antp (see Chapter 4, section 4.2.4). Alternatively, it may

completely change the factor from activator to repressor as in the case of

the dorsal/DSP1 interaction (see Chapter 8, section 8.3.3). Hence, by altering

the specificity of particular factors, interactions of this type are likely to play a

crucial role in the complex regulatory networks which allow a relatively small

number of transcription factors to control highly complex processes such as

development.

As well as such regulatory interactions between different factors it has

become increasingly clear in recent years that many activating transcription

factors need to interact with other factors, such as the mediator complex and/

or co-activators in order to stimulate transcription. The most important of

such co-a ctivators, CBP , was originally characterized as being required for

transcriptional activation in response to cyclic AMP treatment, mediated via

the CREB transcription factor (see Chapter 5, section 5.4.3). It is also

involved, however, in transcriptional activation mediated via a number of

other transcription factors activated by different signalli ng pathways. In

turn, because of the limiting amounts of CBP in the cell, the different tran-

scription factors and signalling pathways compete for CBP resulting in mutual

antagonism between, for example, the signalling pathways mediated by AP1

and the glucocorticoid receptor (see Chap ter 6, section 6.5) .

Thus, the critical dependence of many activating factors on a specific co-

activator can result in a functional link between two different factors which do

not themselves interact but which comp ete for the same co-activator.

Moreover, the activity of a transcription factor can be regulated by controlling

its ability to interact with its co-activator. For example, in the absence of

thyroid hormone, the thyroid hormone receptor has an inhibitory effect on

transcription because it binds co-repressor molecules which act to inhibit

transcription. Following exposure to thyroid hormone however, the receptor

undergoes a conformational change which allows it to bind co-activator mole-

cules and hence activate transcription (see Chapter 6, section 6.3.2). Similarly,

only the phosphorylated form of CREB can interact with CBP and therefore

activate transcription, whereas the non-phosphorylated form does not interact

with CBP and is thus inactive (see Chapter 5, section 5.4.3).

This regulation of CREB by phosphorylation is only one example of a

plethora of post-translational modifications which have been shown in recent

years to modulate transcription factor activity. In addition to phosphorylation,

these modifications include methylation, acetylation and ubiquitination.

Moreover, they have been shown to modify transcription factor activity via

altering processes as diverse as DNA binding, cellular localization and stability

342 EUKARYOTIC TRANSCRIPTION FACTORS

as well as via modulating their interaction with other factors (see Chapter 8,

section 8.4).

Moreover, individual factors can be modulated by more than one post-

translational modification as seen in the cases of the oncogenic transcription

factor -catenin (see Chapter 9, section 9.4.4) and the anti-oncogenic tran-

scription factors, p53 (see Chapter 9, sectio n 9.4.2) and Rb-1 (see Chapter 9,

section 9.4.3). Similarly, these modifications can also target co-activators as

well as DNA binding transcription factors. Thus, as discussed in Chapter 8

(section 8.4.4), CBP can be modified by methylation and phosphorylation and

this differentially affects its binding to different activating transcription

factors. The competition between different activators for binding to CBP

can therefore be regulated by modifying CBP itself, as well as by modifying

the transcription factors themselves.

Hence, the interaction between activators and co-activ ators plays a critical

role in the activation of transcription and its regulation. Although co-activa-

tors are likely to act in some cases by interacting with the basal transcriptional

complex (see Chapter 5, section 5.3), the finding that many co-activators have

histone acetyltransferase activity (see Chapter 5, section 5.5.1) indicates that

they may stimulate transcript ion via altering chromatin structure. Hence such

factors could act by acetylating histones thereby altering the chromatin struc-

ture to a more open structure able to support active transcription (see

Chapter 1, section 1.2.3). Similarly, activators and co-activators may also

recruit chromatin remodelling complexes such as SWI/SNF which use ATP-

dependent processes to open up the chromatin (see Chapter 1, section 1.2.2

and Chapter 5, section 5.5.1). Conversely, co-repressors which have histone

deacetylase activity may act by producing a more closed chromatin structure

incompatible with transcription (see Chapter 6, section 6.4.1).

The activation of a target promoter is likely therefore to require the recruit-

ment of activating molecules, histone acetyltransferases and chromatin remo-

delling complexes as well as of the basal transcriptional complex. As discussed

in Chapter 5 (section 5.6) this is a highly ordered process and at each promo-

ter, a series of events will occur with the recruitment of each factor facilitating

the next stage in the transcription activation process.

Ultimately, therefore, the understanding of transcription factor function

will require a knowledge of the nature and effect of interactions between

different transcription factors, their co-activators and co-repressors which is

as good as that now available for individual factors. Moreover, it will be

necessary to establish how such changes modulate the activity of the basal

transcriptional complex and alter chromatin structure. Clearly much work

remains to be done before this is achieved. The rapid progress since the

first edition of this work was published suggests, however, that an eventual

CONCLUSIONS AND FUTURE PROSPECTS 343

understanding in molecular terms of the manner in which transcription fac-

tors control highly complex processes such as Drosophila and even mammal ian

development can ultimately be achieved.

344 EUKARYOTIC TRANSCRIPTION FACTORS

INDEX

a1 protein, 2 interaction, repressive

effects, 89–90

Acanthamoeba, transcription, 58–60, 62

ACE1, 255

copper-induced activation, 247, 249

Acetylation, 272–4

histones, 5–7

phosphorylation interaction, 274

protein, 273

transcription factors, 272

‘Acid blobs’, 138

Acidic activation domains, 137–9, 140–1

Activation domains, 135–6, 174

acidic, 137–9, 140–1

basal transcriptional complex

interaction, 142–3

chromatin remodelling and, 167–8

co-activator interactions, 149–61

domain-swop experiments, 44–5, 135

factor activity, 146–9

factor binding, 143–6

function of different, 140–1

glutamine-rich, 137, 139–40, 140–1

ligand binding domain and, 253, 255

nature of, 136–41

proline-rich, 137, 140–1

Activation of transcription, 135–81, 342

chromatin remodelling and, 162–70,

173

by stimulation of elongation, 170–4

targets for transcriptional activators,

161–2

see also DNA binding

bax gene, 321

bcl-3 oncogene, 312

Bicoid (bcd)

concentration gradient, 227–9

DNA binding specificity, 84

as morphogen, 228

phosphorylation, 270

regulation, 228

Bithorax, expression patterns, 221–2

Bithorax-Antennapedia complex, 92

Blood pressure, high, 297

Blood vessel growth, 106

Bone development, 246

Brahma mutation, 3, 164

BRCA-1 anti-oncogene, 328

BRCA-2 anti-oncogene, 328

Breast cancer, 328

Brn-3, 46

Brn-3a, 99

Brn-3b, 99

Brn-4, 99

Burkitt’s lymphoma, 312

C/EBP

DNA-binding domain, 117, 119, 120,

125–6

gene cloning, 39–40

regulation of synthesis, 231, 239–40

CAAT box sequence, 126

Caenorhabditis elegans, homeobox genes,

90–1

Calcium, 271

binding to DREAM, 249, 267

Cancer, 297–331

anti-oncogenes and, 314–31

chromosomal translocations, 312, 313,

331

oncogenes and, 299–314, 331–2

role of Fos/Jun, 301–3, 306–7, 308

role of viral ErbA protein, 306–7, 308

Cap site, 8

346 INDEX

-Catenin, 328–30, 332–3

Caudal, 228

CBP (CREB-binding protein), 273, 342,

343

competition for, 206, 303–4, 321

CREB interaction, 157–8, 159–60,

160–1, 267

inhibiting transcription, 329

methylation, 274, 275

mutations, 295–6

p53 requirements, 321

phosphorylation, 274

steroid receptor interactions, 167

CCAAT box, 8, 9

CCAAT box transcription factor, see

CTF/NF1

CCAAT/enhancer binding protein, see

C/EBP

CD4, 16

CDK9 kinase enzyme, 172

Cell cycle, Rb-1 phosphorylation, 323–4

Cell division, inhibition by MyoD, 216

Cell type-specific expression of

transcription factor, 230–1, 238

Cell type-specific gene expression, 211

regulation, 245, 285

CF1a, 99

Chaperone protein, 260

ChIP (chromatin immunoprecipitation)

assay, 48–50, 143

Cholesterol, 282, 283

Chromatin, 2–7

remodelling

in activation of transcription,

162–70, 173, 343

factors, 3–5

histone acetyltransferases in, 68

MyoD-mediated, 215–16

in repression of transcription, 200–3

during transcription, 66, 68

structure, 2–3

histone acetylation/modification

and, 5–7

modulation of, 200–3, 324, 343

mutations in factors altering, 294,

295, 297

Chromatin immunoprecipitation (ChIP)

assay, 48–50, 143

Chromosomal translocations, 312, 313,

331

cis-trans isomerization, 318

CLIM co-activator molecule, 197–8

Cloning, genes, 38–41

protein production from cloned genes,

use of cloned genes, 41–50

Co-activators, 68, 149–61, 253, 342–3

co-repressor interchange, 197–8

competition for, 206

histone acetyltransferase activity,

160–1, 176, 215

methylation, 274

mutations, 295, 297

Co-repressors, 343

co-activator interchange, 197–8

histone deacetylase activity, 202

inhibitory domains and, 196–7

Collagenase gene, 205–6, 303

Colon tumours, 328

Complementary DNA (cDNA)

clones

applications, 41–50

isolation, 38–41

libraries, 38, 39, 40

Copper, 247

Corticosterone, 250

CRE (cyclic AMP response element),

157–8, 186, 233, 235, 236

Creatine kinase (CK), 188

Creatine kinase gene, 215

CREB (cyclic AMP response element

binding protein), 233, 234, 235,

236, 342

CBP interaction, 157–8, 159–60, 160–1,

267

Jun interaction, 264

phosphorylation, 158–9, 266, 267, 342

CREB-binding protein, see CBP

CREM, 285

activating/inhibiting forms, 233–5, 236

phosphorylation, 267

promoters, 234–5

CTF/NF1

activation domains, 137, 140

binding sites, 166

DNA-binding domain, 124, 125–6

INDEX 347

CTF/NF1 (cont.)

gene cloning, 38

purification, 36–8

CYC1, 142

Cyclic AMP-inducible genes, 266

Cyclic AMP-inducible transcription, 1

Cyclic AMP response element (CRE),

157–8, 186, 233, 235, 236, 264

Cyclic AMP response element binding

protein, see CREB

Cyclin-dependent kinases, 324–5

p21 inhibitor, 216, 320

Cyclin genes, 155

Cycloheximide, 245, 258

Cyp40, 318

D2 gene, 328

DBP, 231

Dbx1, 225, 226

Dbx2, 225, 226

Deafness, 99, 101

Decapentaplegic (dpp) gene, 89

Deformed gene, 92

Degradation, protein

regulation, 281–3

repression by, 190–1

ubiquitination and, 275–6, 277, 279

Demethylation, 212–13

Deoxyribonuclease I, see DNase I

Developmental disorders, human, 293–7

Developmentally regulated gene

expression, 211, 285

Diabetes, 297

Diethylpyrocarbonate, 31

Dimerization

disulphide bond-mediated, 119

helix-loop-helix-mediated, 121–2

leucine zipper-mediated, 117, 118, 120

in regulation of activity, 251, 252

role in DNA binding, 122–4

Dimethyl sulphate (DMS)

in vivo footprinting assay, 33

methylation interference assay, 30–2

protection footprinting, 29–30

2, 4-Dinitrophenol (DNP), 258

Disease, human, 293–340

Disulphide bridges, 119, 120

Diurnal variations, 231

DNA

affinity chromatography, 34–5

bending, factors causing, 18–19

competitor, 25–7, 28

complementary, see Complementary

DNA

looping, 2–3, 4–5, 17, 18

methylation, 212

packaging, 2

protein interactions, methods of study,

23–34

repair, 65

DNA binding, 39

homeobox proteins, 86, 88–90

leucine zipper/basic domain, 117–24

mapping methods, 43

motifs, 124–5, 125–7

not activating transcription, 43

repression mechanisms, 183–7

specificity, uncharacterized factor,

45–7

by transcription factors, 127

zinc finger motif, 104–16