"Frontmatter". In: Plant Genomics and Proteomics

E
FFECTS OF
C
HROMATIN
S
TRUCTURE
It is clear that chromatin (the proteinaceous material that together with DNA
comprises the chromosomes) structure is not just a mechanism for conve-
niently packaging the DNA within the nucleus. The chromatin is a dynamic
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5. C
O N T R O L O F
G
E N E
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T
ABLE 5.3. S
TRENGTHS
AND
L
IMIT
A
TIONS
OF
C
HEMICALL
Y
R
EGULA
TED
S
YSTEMS
D
EVELOPED
FOR
P
LANT
G
ENE
E
XPRESSION
System
T
ested in
Str
engths
Limitations
T
etracycline-
T
obacco, tomato, 
Low amounts of inducer ar
e 
Leaky expr
ession, high concentrations
inducible T
etR
potato, BY2 cells,
suf
ficient for activation, 
of T
etR ar
e r
equir
ed, short half-life
SR1 cells
inducer r
eadily taken up
of inducer
, does not work in
by cells
Arabidopsis
T
etracycline-
Arabidopsis
, tobacco,
T
ar
get pr
omoter can be shut 
Plants must be maintained with
inactivatable tT
A
NT1 cells
of
f ef
ficiently
, turnover of
tetracycline to turn of
f gene
transgene can be assessed,
expr
ession, negatively contr
olled
lower basal levels compar
ed
system
with T
etR
Dexamethasone-
Arabidopsis
, tobacco
GR::transcription factor fusion
Only suitable for transcription factors,
inducible GR
pr
oteins identify immediate
inducer toxic in some cases, 
fusions
tar
get genes, 
induction of defense-r
elated genes 
posttranscriptional
in 
Arabidopsis
activation
Dexamethasone-
Arabidopsis
, tobacco
Dexamethasone easily 
Inducer toxic in some cases, induction
inducible GVG
permeates plants cells and 
of defense-r
elated genes in 
can be applied by various
Arabidopsis
, slow of
f rate
routes
Estradiol-inducible
Black Mexican sweet 
Relatively low levels of 
Not tested in transgenic plants, not 
ER–C1
corn cells
estradiol ar
e r
equir
ed, no 
suitable for plants with 
appar
ent toxic ef
fects
phytoster
oids
Estradiol-inducible 
Arabidopsis
, tobacco,
No appar
ent toxic ef
fects, 
Not suitable for plants with 
XVE
BY2 cells
low basal level and high
phytoster
oids (soybean), not
inducible levels
suitable for field use

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Dex-inducible and 
Arabidopsis
, tobacco, 
Dual contr
ol, quick shut of
f 
Inducer toxic in some cases, defense-
tet-r
epr
essible TGV
BY2 cells
related genes may be induced
T
ebufenozide-
T
obacco
Safe inducer
, suitable for field 
High basal activity
, foliar uptake of 
inducible
application
inducer is poor
GVHvEcR
Methoxyfenozide-
Arabidopsis
, tobacco, 
Low basal and high inducible 
Foliar uptake of inducer is poor
, turn
inducible
BY2 cells
levels, safe inducer
, suitable 
of
f is slow
GVCfEcR
for field application
Methoxyfenozide-
Maize
Safe inducer
, inducer moves 
Foliar uptake of inducer is poor
inducible
systemically
, suitable for 
GVOnEcR
field application
Ethanol-inducible 
Arabidopsis
, tobacco, 
Inducer inexpensive and 
V
olatile inducer
, induction can 
AlcR
potato
biodegradable, rapid 
trigger
ed inadvertently
, induction 
reversible induction, 
due to anoxia, inducer cannot be 
suitable for field application
used for mor
e than 2 d
Copper
-inducible 
Arabidopsis
, tobacco, r
oot
Ease of application of inducer
, 
Induced levels ar
e low
, long exposur
e
ACEI
nodules, BY2 cells
simple to use, inducer 
of inducer is toxic, does not work 
inexpensive
in BY2 or pr
otoplasts derived fr
om
tobacco leaves, expr
ession is
variable in 
Arabidopsis
Benzothiadiazole-
T
obacco
Inducer not phytotoxic, long-
Low induction levels, pr
omoter also
inducible PR-1a
lasting r
esponse, suitable for
responds to oxidative str
ess and 
expr
ession of disease 
endogenous salicylic acid signals,
resistance genes in field
inducer activates native genes
Safener
-inducible
Arabidopsis
, BY2 cells
Suitable for field application, 
Inducer causes gr
owth abnormalities,
In2-2
inducer is an agr
ochemical
constitutive expr
ession in r
oots, 
pr
omoter r
esponsive to other
chemicals
Reprinted fr
om 
Curr
. Opin. Plant Biol.
6, Padidam, Chemically r
egulated gene expr
ession in plants, 169–177, Copyright 2003, with permission
fr
om Elsevier
.

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material that changes as the internal cellular environment alters, whether in
response to the external environment or to endogenous changes. A key
requirement for the expression of genes in chromosomes is that chromatin
be remodeled (i.e., “opened”) in such a way that transcriptional activator
proteins and RNA polymerases can have access to the DNA, permitting the
assembly of a transcription complex that then transcribes the gene into mes-
senger RNA.
The nucleosome, in which a loop of DNA about 150 nucleotides long is
wrapped around a core of histone proteins, is the basic unit of chromatin.
This histone core consists of an octamer containing two copies of each of the
four histones H2A, H2B, H3, and H4. The nucleosomes are packaged in suc-
cessively higher orders of coiling in the chromosomes. The changes in chro-
matin structure are mediated through modifications to the histones that
include acetylation, phosphorylation, ubiquitination, and ADP-ribosylation
of particular amino acid residues. The role of the Arabidopsis gene DDM1
(Decrease in DNA Methylation 1) indicates that the chromatin modification
can also be intimately involved with DNA methylation (Singer et al., 2001). 
The change in chromatin state, in itself, does not necessarily result in the
transcription of the region but simply alters the accessibility of the region.
Therefore, it is still necessary for the appropriate trans-acting factors, such
as transcription factors, to be present for the gene transcription to occur. Con-
versely, however, the lack of chromatin remodeling can prevent gene tran-
scription even in the presence of the appropriate trans-acting factors.
Matrix attachment regions (MARs) that flank some plant genes may also
be necessary for the correct regulation of those genes. For example, the
MARs in addition to the downstream region and introns from the heat shock
cognate 80 gene (HSC80) of tomato are necessary for the efficient expression
of HSC80 transgenes (Holmes-Davis and Comai, 2002). The MARs are iden-
tified by their ability to bind the nuclear matrix and are AT rich. They also
include the topoisomerase II consensus sequence. Two possible methods by
which MARs may exert their influence are:
∑ By anchoring the ends of chromatin loops to the nuclear matrix and
resulting in an independent chromatin domain
∑ MARs might be important for interactions between the activating
complexes and the DNA
In the first case MARs should be nonspecific and function to activate
most genes, whereas in the second case the effects are more likely to be gene
specific. These two effects may not be mutually exclusive, nor is it necessary
that all MARs function in the same manner. Support for the role of MARs in
the interaction with gene-specific elements for the induction of transcrip-
tional competence and therefore a limited role in heterologous contexts has
been reported (Holmes-Davis and Comai, 2002). 
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