"Frontmatter". In: Plant Genomics and Proteomics

CHAPTER
5
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VERVIEW
The control of gene expression can occur at many levels (Figure 5.1). The
primary level involves the transcription of the DNA into RNA. There are
many controls over the initiation of this event including the need for pro-
moters and terminator sequences, for appropriate chromatin structure and
the presence of enhancers or modulating sequences that affect the availabil-
ity of a particular gene for transcription. Once transcribed the RNA then
must be processed into a mature message and exported from the nucleus in
a form that permits translation by the ribosomal machinery. The half-lives
of various RNAs, and even their capability of being translated, differ widely.
After translation the RNAs can either be recycled and translated again or
can be targeted for degradation. The final points of control are at the protein
level with protein modification events that affect the ultimate function of the
protein product of the gene. 
Not all genes are turned on at all times during the life cycle of a plant.
Different genes are required for the completion of different steps in the devel-
opmental and sexual maturation of the plant and in response to the 
external environment (see Chapter 7). Two general types of control can 
be described: 
∑ Temporal regulation—when a gene is only expressed at a specific
time in development, for example, genes that are only expressed in
the light or during flower development 
∑ Spatial regulation—when a gene is only expressed in a specific loca-
tion in the plant, for example, seed storage proteins or anther specific
genes 
Plant Genomics and Proteomics, by Christopher A. Cullis
ISBN 0-471-37314-1 Copyright © 2004 John Wiley & Sons, Inc.
8 9

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Gene expression is controlled by both the sequences surrounding the
gene and the chromosome context in which the gene resides. The promoter
elements can be complex containing sequences that control temporal and
spatial regulation as well as enhancer and silencing activities. Added to these
9 0
5. C
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chromatin
exon
intron
DNA
Transcription
pre-mRNA
mRNA
Processing
transport
Protein modification
Protein degradation
AAAAAA
RNA degradation
translation
5'
5'
nuclear membrane
FIGURE 5.1.
Points of control in gene expression. The region of the chromosome to
be transcribed accumulates RNA polymerase. The nascent RNA is processed and
then transported to the cytoplasm to be translated. The RNA is degraded or reused.
The peptide is folded and/or modified to deliver the final product that is itself
degraded at some point.

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elements, the role of 3¢ sequences and introns in gene expression also must
be considered. Chromatin variation brought about by the reversible modifi-
cation of the core histones by acetylation, methylation, phosphorylation,
ubiquitination, or ADP-ribosylation (Strahl and Allis, 2000) all have conse-
quences for gene activation, gene repression, and chromosome replication.
Epigenetic phenomena are alternative states of gene expression, molecular
function, or organization specified by the same genetic instructions (the
primary DNA sequence). Chromatin modifications including cytosine
methylation and histone modifications are known to be involved in many
such epigenetic phenomena (Habu et al., 2001).
Many of the experiments to determine the nature of control elements
have been done by making transgenic plants. Unfortunately, high-efficiency
homologous recombination is not currently available in plants so that it is
not possible to place such control elements in their appropriate chromoso-
mal context. This raises concerns because it is clear that the chromosomal
context counts for the appropriate expression patterns to be reproduced, so
that the expression patterns observed with transgenic plants may not accu-
rately reflect the normal in vivo situation (Li et al., 2002).