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4: Gene Regulation in Eukaryotic Cells Takes Place at Multiple Levels

4: Gene Regulation in Eukaryotic Cells Takes Place at Multiple Levels

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Histone protein

Control of Gene Expression
1 Positively charged tails of
nucleosomal histone
proteins probably interact
with the negatively charged
phosphate groups of DNA.


Arabidopsis, a plant with a number of characteristics that
make it an excellent genetic model for plant systems (see
the section at the end of this chapter on the model genetic
organism Arabidopsis thaliana). The time at which flowering takes place is critical to the life of a plant; if flowering
is initiated at the wrong time of year, pollinators may not
be available to fertilize the flowers or environmental conditions may be unsuitable for survival and germination of
the seeds. Consequently, flowering time in most plants is
carefully regulated in response to multiple internal and
external cues, such as plant size, photoperiod, and
Among the many genes that control flowering in
Arabidopsis is flowering locus C (FLC), which plays an
important role in suppressing flowering until after an
extended period of coldness (a process called vernalization).
The FLC gene encodes a transcriptional activator protein,
which acts on other genes that affect flowering (Figure 12.14).

charged tail

2 Acetylation of the tails
weakens their interaction
with DNA and may permit
some transcription factors
to bind to DNA.


12.13 The acetylation of histone proteins alters chromatin
structure and permits some transcription factors to bind
to DNA.





1 Acetyl groups on
histone proteins
destabilize chromatin
2 Flowering locus C
(FLC ) encodes
a transcriptional
activator protein that
represses flowering.

activator protein


5 …that removes acetyl
groups and restores
chromatin structure.

3 No flowering
takes place.


4 Flowering locus D
(FLD) encodes a
deacetylase enzyme…

6 No transcription or
translation of FLC
takes place.

of chromatin
No transcription

No translation

7 Flowering is not
suppressed, and so
flowering takes place.

12.14 Flowering in Arabidopsis is controlled in part by FLD, a gene that
encodes a deacetylase enzyme. This enzyme removes acetyl groups from histone
of flowering

proteins in chromatin surrounding FLC, a gene that suppresses flowering. The removal
of the acetyl groups from the histones restores chromatin structure and represses the
transcription of FLC, thereby allowing the plant to flower.

No repressing
of flowering



Chapter 12

As long as FLC is active, flowering remains suppressed. The
activity of FLC is controlled by another locus called flowering locus D (FLD), the key role of which is to stimulate
flowering by repressing the action of FLC. How does FLD
repress FLC?
FLD encodes a deacetylase enzyme, which removes
acetyl groups from histone proteins in the chromatin surrounding FLC (see Figure 12.14). The removal of acetyl
groups from histones restores chromatin structure and
inhibits transcription. The inhibition of transcription
prevents FLC from being transcribed and removes its
repression on flowering. In short, FLD stimulates flowering in Arabidopsis by deacetylating the chromatin that surrounds FLC, thereby removing its inhibitory effect on

Chromatin remodeling The changes to chromatin
structure discussed so far have been through alteration of
the structure of the histone proteins. Some transcription
factors and other regulatory proteins alter chromatin
structure without altering the chemical structure of the
histones directly. These proteins are called chromatinremodeling complexes. They bind directly to particular
sites on DNA and reposition the nucleosomes, allowing
transcription factors to bind to promoters and initiate
One of the best-studied examples of a chromatinremodeling complex is SWI–SNF, which is found in yeast,
humans, Drosophila, and other organisms. This complex utilizes energy derived from the hydrolysis of ATP to reposition
nucleosomes, exposing promoters in the DNA to the action
of other regulatory proteins and RNA polymerase. Research
has shown that SWI–SNF is able to change the position of
nucleosomes along a DNA molecule.

DNA methylation Another change in chromatin structure associated with transcription is the methylation of
cytosine bases, which yields 5-methylcytosine. The methylation of cytosine in DNA is distinct from the methylation of
histone proteins mentioned earlier. Heavily methylated
DNA is associated with the repression of transcription in
vertebrates and plants, whereas transcriptionally active
DNA is usually unmethylated in these organisms. Abnormal
patterns of methylation are also associated with some types
of cancer.

Transcription Factors and
Transcriptional Activator Proteins
Transcription is an important level of control in eukaryotic
cells, and this control requires a number of different types of
proteins and regulatory elements. General transcription
factors and RNA polymerase assemble into a basal
transcription apparatus, which binds to a core promoter
located immediately upstream of a gene. The basal transcription apparatus is capable of minimal levels of transcription;
transcriptional activator proteins are required to bring
about normal levels of transcription. These proteins bind to
a regulatory promoter, which is located upstream of the core
promoter (Figure 12.15), and to enhancers, which may be
located some distance from the gene.
Transcriptional activator proteins stimulate and stabilize the basal transcription apparatus at the core promoter.
The activators may interact directly with the basal transcription apparatus or indirectly through protein coactivators.
Some activators and coactivators, as well as the general transcription factors, also have acetyltransferase activity and so
further stimulate transcription by altering chromatin structure (see earlier section on histone modification).
Within the regulatory promoter are typically several different consensus sequences to which different transcriptional activators can bind. Among different promoters,
activator-binding sites are mixed and matched in different
combinations (Figure 12.16), and so each promoter is regulated by a unique combination of transcriptional activator
Some regulatory proteins in eukaryotic cells act as
repressors, inhibiting transcription. These repressors bind
to sequences in the regulatory promoter or to distant
sequences called silencers, which, like enhancers, are position and orientation independent. Unlike repressors in
bacteria, most eukaryotic repressors do not directly block
RNA polymerase. These repressors may compete with activators for DNA binding sites: when a site is occupied by an
activator, transcription is activated, but, if a repressor
occupies that site, there is no activation. Alternatively, a
repressor may bind to sites near an activator site and prevent the activator from contacting the basal transcription
apparatus. A third possible mechanism of repressor action
is direct interference with the assembly of the basal transcription apparatus, thereby blocking the initiation of

Chromatin structure can be altered by modifications of histone
proteins, by chromatin-remodeling complexes that reposition
nucleosomes, and by the methylation of DNA.

Transcriptional regulatory proteins in eukaryotic cells can influence the initiation of transcription by affecting the stability or
assembly of the basal transcription apparatus. Some regulatory
proteins are activators and stimulate transcription; others are
repressors and inhibit transcription.

Control of Gene Expression

12.15 Transcriptional activator

Activator-binding site
(regulatory promoter)


Core promoter

proteins bind to sites on DNA and
stimulate transcription. Most act by

TATA box

Transcription factors, RNA
polymerase, and transcriptional
activator proteins bind DNA
and stimulate transcription.

stimulating or stabilizing the assembly of
the basal transcription apparatus.


activator protein





activator protein

Basal transcription apparatus

✔ Concept Check 7
Most transcriptional activator proteins affect transcription by
interacting with
a. introns.

c. DNA polymerase.

b. the basal transcription apparatus.

d. nucleosomes.

the two, it has no effect (Figure 12.17). Specific proteins bind
to insulators and play a role in their blocking activity. Some
insulators also limit the spread of changes in chromatin
structure that affect transcription.

Regulatory promoter

Enhancers and insulators Enhancers are capable of
affecting transcription at distant promoters. For example, an
enhancer that regulates the gene encoding the alpha chain of
the T-cell (T-lymphocyte) receptor is located 69,000 bp
downstream of the gene’s promoter. Furthermore, the exact
position and orientation of an enhancer relative to the
promoter can vary. How can an enhancer affect the initiation
of transcription taking place at a promoter that is tens of
thousands of base pairs away? In many cases, activator proteins bind to the enhancer and cause the DNA between the
enhancer and the promoter to loop out, bringing the promoter and enhancer close to each other, and so the
transcriptional activator proteins are able to directly interact
with the basal transcription apparatus at the core promoter
(see Figure 12.15).
Most enhancers are capable of stimulating any promoter
in their vicinities. Their effects are limited, however, by insulators (also called boundary elements), which are DNA
sequences that block or insulate the effect of enhancers in a
position-dependent manner. If the insulator lies between the
enhancer and the promoter, it blocks the action of the
enhancer; but, if the insulator lies outside the region between

SV40 early promoter


Core promoter



start site
Thymidine kinase promoter

Histone H2B promoter








TATA box

GC box

CAAT box

OCT box



12.16 The consensus sequences in the promoters of three
eukaryotic genes illustrate the principle that different
sequences can be mixed and matched in different
combinations. A different transcriptional activator protein binds
to each consensus sequence, and so each promoter responds to a
unique combination of activator proteins.



Chapter 12

1 Enhancer I can stimulate the
transcription of gene A, but its effect
on gene B is blocked by the insulator.

Gene A


Enhancer I


2 Enhancer II can stimulate the
transcription of gene B, but its effect
on gene A is blocked by the insulator.



Enhancer II

Gene B



12.17 An insulator blocks the action of an enhancer on a promoter when the insulator lies
between the enhancer and the promoter.

Some activator proteins bind to enhancers, which are regulatory
elements that are distant from the gene for which they stimulate
transcription. Insulators are DNA sequences that block the action
of enhancers.

✔ Concept Check 8
How does the binding of transcriptional activator proteins to
enhancers affect transcription at genes that are thousands of base
pairs away?

Coordinated gene regulation Although most eukaryotic
cells do not possess operons, several eukaryotic genes may be
activated by the same stimulus. For example, many eukaryotic cells respond to extreme heat and other stresses by producing heat-shock proteins that help to prevent damage
from such stressing agents. Heat-shock proteins are produced
by a large number of different genes. During times of environmental stress, the transcription of all the heat-shock genes
is greatly elevated. Groups of bacterial genes are often coordinately expressed (turned on and off together) because they
are physically clustered as an operon and have the same promoter, but coordinately expressed genes in eukaryotic cells
are not clustered. How, then, is the transcription of eukaryotic genes coordinately controlled if they are not organized
into an operon?
Genes that are coordinately expressed in eukaryotic
cells are able to respond to the same stimulus because they
have regulatory sequences in common in their promoters or
enhancers. For example, different eukaryotic heat-shock
genes possess a common regulatory element upstream of
their start sites. Such DNA regulatory sequences are called
response elements; they typically contain short consensus
sequences at varying distances from the gene being regulated, which provide binding sites for transcriptional activators. During times of stress, a transcriptional activator
protein binds to this regulatory element and elevates

Gene Regulation by RNA Processing
and Degradation
In bacteria, most gene regulation is at the level of transcription, because transcription and translation take place
simultaneously, leaving little opportunity to control gene
expression after transcription. In eukaryotes, transcription
takes place in the nucleus and the pre-mRNAs are then
processed before moving to the cytoplasm for translation,
and so there are more opportunities for gene control after
transcription. Consequently, posttranscriptional gene regulation assumes a more important role in eukaryotic cells.
One place in eukaryotes where gene expression is frequently
controlled is in RNA processing and degradation.

Gene regulation through RNA splicing Alternative
splicing allows a pre-mRNA to be spliced in multiple ways,
generating different proteins in different tissues or at different times in development (see Chapter 10). Many eukaryotic
genes undergo alternative splicing, and the regulation of
splicing is probably an important means of controlling gene
expression in eukaryotic cells.
An example of alternative mRNA splicing that regulates gene expression is the control of whether a fruit fly
develops as male or female. Sex differentiation in
Drosophila arises from a cascade of gene regulation. When
the ratio of X chromosomes to the number of haploid sets
of autosomes (the X : A ratio; see Chapter 4) is 1, a femalespecific promoter is activated early in development and
stimulates the transcription of the sex-lethal (Sxl) gene
(Figure 12.18). The protein encoded by Sxl regulates the
splicing of the pre-mRNA transcribed from another gene
called transformer (tra). The splicing of tra pre-mRNA
results in the production of Tra protein (see Figure 12.18).
Together with another protein (Tra-2), Tra stimulates the
female-specific splicing of pre-mRNA from yet another
gene called doublesex (dsx). This event produces a femalespecific Dsx protein, which causes the embryo to develop
female characteristics.
In male embryos, which have an X : A ratio of 0.5 (see
Figure 12.18), the promoter that transcribes the Sxl gene in
females is inactive; so no Sxl protein is produced. In the

Control of Gene Expression


XX genotype
X ؒؒ A = 1.0

Female Fly
Tra-2 protein
dsx pre-mRNA

Sxl gene

Sxl protein

1 In X ии A = 1.0 embryos,
the activated Sxl gene
produces a protein…

Tra protein

tra pre-mRNA

2 …that causes tra premRNA to be spliced at
a downstream 3‘ site…


3 …to produce
Tra protein.

4 Together, Tra and Tra-2 proteins
direct the female-specific
splicing of dsx pre-mRNA,…

5 …which produces proteins
causing the embryo to
develop into a female.

XY genotype
X ؒؒ A = 0.5
Sxl gene

Male Fly
No Sxl

1 In X ии A = 0.5 embryos, the Sxl
gene is not activated, and the Sxl
protein is not produced.

tra pre-mRNA


Tra protein

dsx pre-mRNA

3 …producing a
Tra protein.

4 Without Tra, the malespecific splicing of dsx

2 Thus, tra pre-mRNA
is spliced at an
upstream site,…

5 …produces male Dsx proteins
that cause the embryo to
develop into a male.

12.18 Alternative splicing controls sex determination in Drosophila.

absence of Sxl protein, tra pre-mRNA is spliced at a different
3Ј splice site to produce a nonfunctional form of Tra protein
(Figure 12.19). In turn, the presence of this nonfunctional
Tra in males causes dsx pre-mRNAs to be spliced differently
from that in females, and a male-specific Dsx protein is produced (see Figure 12.18). This event causes the development
of male-specific traits.
In summary, the Tra, Tra-2, and Sxl proteins regulate
alternative splicing that produces male and female phenotypes in Drosophila. Exactly how these proteins regulate
alternative splicing is not yet known, but the Sxl protein
(produced only in females) possibly blocks the upstream
splice site on the tra pre-mRNA. This blockage would force
the spliceosome to use the downstream 3Ј splice site, which
causes the production of Tra protein and eventually results
in female traits (see Figure 12.19).

Eukaryotic genes can be regulated through the control of mRNA
processing. The selection of alternative splice sites leads to the
production of different proteins.

The degradation of RNA The amount of a protein that
is synthesized depends on the amount of corresponding
mRNA available for translation. The amount of available
mRNA, in turn, depends on both the rate of mRNA synthesis and the rate of mRNA degradation. Eukaryotic mRNAs

are generally more stable than bacterial mRNAs, which typically last only a few minutes before being degraded.
Nonetheless, there is great variability in the stability of
eukaryotic mRNA: some mRNAs persist for only a few minutes; others last for hours, days, or even months. These variations can result in large differences in the amount of protein
that is synthesized.
Various factors, including the 5Ј cap and the poly(A)
tail, affect the stability of eukaryotic mRNA. Poly(A)-binding proteins (PABPs) normally bind to the poly(A) tail and
contribute to its stability-enhancing effect. The presence of
these proteins at the 3Ј end of the mRNA protects the 5Ј cap.
When the poly(A) tail has been shortened below a critical
limit, the 5Ј cap is removed, and the mRNA is degraded by
removal of nucleotides from the 5Ј end. These observations
suggest that the 5Ј cap and the 3Ј poly(A) tail of eukaryotic
mRNA physically interact with each other, most likely by the
poly(A) tail bending around so that the PABPs make contact
with the 5Ј cap.
Much of RNA degradation takes place in specialized
complexes called P bodies. P bodies help control the
expression of genes by regulating which RNA molecules
are degraded and which are sequestered for later release.
RNA degradation facilitated by small interfering RNAs
(siRNAs) also may take place within P bodies (see next
Other parts of eukaryotic mRNA, including sequences
in the 5Ј untranslated region (5Ј UTR), the coding region,
and the 3Ј UTR, also affect mRNA stability. Some short-lived
eukaryotic mRNAs have one or more copies of a consensus


Chapter 12

Alternative 3’ splice sites
tra pre-mRNA 5’


1 In females, the presence
of Sxl protein causes the
downstream 3‘ splice
site to be used,…


1 In males, the
upstream 3‘
splice site is

Sxl protein


2 …and the termination
codon is spliced out
with the intron.




mRNA 5’




3’ 5’


Premature stop codon

2 …resulting in the
inclusion of a
premature stop
codon in the mRNA.


Tra protein
3 No functional Tra
protein is produced.

Tra protein
3 A functional Tra
protein is produced.

12.19 Alternative splicing of tra pre-mRNA. Two alternative 3Ј
splice sites are present.

sequence consisting of 5Ј-AUUUAUAA-3Ј, referred to as the
AU-rich element, in the 3Ј UTR. The mRNAs containing
AU-rich elements are degraded by a mechanism in which
microRNAs take part (see next section).

The stability of mRNA influences gene expression by affecting the
amount of mRNA available to be translated. The stability of mRNA
is affected by the 5Ј cap, the poly(A) tail, the 5Ј UTR, the coding
section, and sequences in 3Ј UTR.

✔ Concept Check 9
How does the poly(A) tail affect stability?

RNA Interference and Gene
The expression of a number of eukaryotic genes is controlled
through RNA interference, also known as RNA silencing and
posttranscriptional gene silencing (see Chapter 10). Recent
research suggests that as much as 30% of human genes are
regulated by RNA interference. Although many of the details
of this mechanism are still poorly understood, RNA interference appears to be widespread, existing in fungi, plants, and
animals. This technique is also widely used as a powerful tool
for artificially regulating gene expression in genetically engineered organisms (see Chapter 14).
RNA interference is triggered by small RNA molecules
know as microRNAs (miRNAs) and small interfering RNAs
(siRNAs), depending on their origin and mode of action (see
Chapter 10). An enzyme called Dicer cleaves and processes
double-stranded RNA to produce siRNAs or miRNAs that
are from 21 to 25 nucleotides in length (Figure 12.20) and
pair with proteins to form an RNA-induced silencing
complex (RISC). The RNA component of the RISC then
pairs with complementary base sequences of specific mRNA
molecules, most often with sequences in the 3Ј UTR of the
mRNA. Small interfering RNAs and microRNAs regulate
gene expression through at least three distinct mechanisms:
(1) cleavage of mRNA, (2) inhibition of translation, or (3)
transcriptional silencing.

RNA cleavage RISCs that contain an siRNA (and some
that contain an miRNA) pair with mRNA molecules and
cleave the mRNA near the middle of the bound siRNA (see
Figure 12.20a). This cleavage is sometimes referred to as
“Slicer activity.” After cleavage, the mRNA is further
degraded. Thus, the presence of siRNAs and miRNAs
increases the rate at which mRNAs are broken down and
decreases the amount of protein produced.
Inhibition of translation Some miRNAs regulate genes
by inhibiting the translation of their complementary
mRNAs (see Figure 12.20b). For example, an important gene
in flower development in Arabidopsis thaliana is APETALA2.
The expression of this gene is regulated by an miRNA that
base pairs with nucleotides in the coding region of
APETALA2 mRNA and inhibits its translation.
Transcriptional silencing Other siRNAs silence transcription by altering chromatin structure. These siRNAs
combine with proteins to form a complex called RITS (for
RNA transcriptional silencing), which is analogous to RISC
(see Figure 12.20c). The siRNA component of a RITS then
binds to its complementary sequence in DNA or an RNA
molecule in the process of bring transcribed and represses
transcription by attracting enzymes that methylate the
tails of histone proteins. The addition of methyl groups to
the histones causes them to bind DNA more tightly,

Control of Gene Expression

Double-stranded RNA




1 Doublestranded RNA
is cleaved by the
enzyme Dicer…
2 …to produce
small interfering
RNAs (siRNAs).





3 The siRNAs
with protein
complex RISC…



Double-stranded region of RNA



1 Other doublestranded regions
of RNA molecules
are cleaved
by Dicer…



2 …to produce
3 Some miRNAs
combine with
protein complex
RISC and pair
with an mRNA…


4 …and pair with
on mRNA.

6 After cleavage, the
RNA is degraded.

1 Other miRNAs
attach to
sequences in
DNA and attract



4 …which leads to
the inhibition
of translation.

5 The complex
cleaves the mRNA.



Inhibition of

Inhibition of

2 …which
methylate the
DNA or histones
and inhibit

12.20 RNA silencing leads to the degradation of mRNA or to the inhibition of translation
or transcription. (a) Small interfering RNAs (siRNAs) degrade mRNA by cleavage. (b) MicroRNAs
(miRNAs) lead to the inhibition of translation. (c) Some siRNAs methylate histone proteins or DNA,
inhibiting transcription.

restricting the access of proteins and enzymes necessary to
carry out transcription (see earlier section on histone

RNA silencing is initiated by double-stranded RNA molecules that
are cleaved and processed. The resulting siRNAs or miRNAs combine with proteins to form complexes that bind to complementary
sequences in mRNA or DNA. The siRNAs and miRNAs affect gene
expression by cleaving mRNA, inhibiting translation, or altering
chromatin structure.

✔ Concept Check 10

mRNAs is regulated by proteins that bind to an mRNA’s 5Ј
UTR and inhibit the binding of ribosomes, in a fashion similar to the way in which repressor proteins bind to operators
and prevent the transcription of structural genes. The translation of some mRNAs is affected by the binding of proteins
to sequences in the 3Ј UTR.
Many eukaryotic proteins are extensively modified after
translation by the selective cleavage and trimming of amino
acids from the ends, by acetylation, or by the addition of
phosphate groups, carboxyl groups, methyl groups, or carbohydrates to the protein. These modifications affect the
transport, function, and activity of the proteins and have the
capacity to affect gene expression.

In RNA silencing, siRNAs and miRNAs usually bind to which part of
the mRNA molecules that they control?


a. 5Ј UTR

c. 3Ј poly(A) tail

b. 5’ cap

d. 3Ј UTR

The initiation of translation may be affected by proteins that bind
to specific sequences near the 5Ј end of mRNA. The availability of
ribosomes, tRNAs, initiation and elongation factors, and other
components of the translational apparatus may affect the rate of

Gene Regulation in the Course
of Translation and Afterward
Ribosomes, aminoacyl tRNAs, initiation factors, and elongation factors are all required for the translation of mRNA
molecules. The availability of these components affects the
rate of translation and therefore influences gene expression.
Mechanisms also exist for the regulation of translation
of specific mRNAs. The initiation of translation in some

Connecting Concepts
A Comparison of Bacterial and Eukaryotic Gene Control
Now that we have considered the major types of gene regulation in
bacteria and eukaryotes, let’s pause to consider some of the similarities and differences in bacterial and eukaryotic gene control.


Chapter 12

1. Most gene regulation in bacterial cells is at the level of transcription
(although it does exist at other levels). Gene regulation in
eukaryotic cells most often takes place at multiple levels, including
chromatin structure, transcription, mRNA processing, RNA stability,
RNA interference, translation, and posttranslational control.
2. Complex biochemical and developmental events in bacterial and
eukaryotic cells may require a cascade of gene regulation, in which
the activation of one set of genes stimulates the activation of
another set.
3. Much of gene regulation in both bacterial and eukaryotic cells
is accomplished through proteins that bind to specific sequences
in DNA.
4. Chromatin structure plays a role in eukaryotic (but not bacterial)
gene regulation. In general, condensed chromatin represses
gene expression; chromatin structure must be altered before
transcription can take place. Chromatin structure is altered by the
modification of histones, chromatin-remodeling proteins, and DNA
5. In bacterial cells, genes are often clustered in operons and are
coordinately expressed by transcription into a single mRNA
molecule. In contrast, each eukaryotic gene typically has its own
promoter and is transcribed independently. Coordinate regulation
in eukaryotic cells takes place through common response
elements, present in the promoters and enhancers of the genes.
Different genes that have the same response element in common
are influenced by the same regulatory protein.
6. Regulatory proteins that affect transcription exhibit two basic
types of control: repressors inhibit transcription (negative control);
activators stimulate transcription (positive control). Both negative
control and positive control are found in bacterial and eukaryotic
7. The initiation of transcription is a relatively simple process in
bacterial cells, and regulatory proteins function by blocking or
stimulating the binding of RNA polymerase to DNA. In contrast,
eukaryotic transcription requires complex machinery that includes
RNA polymerase, general transcription factors, and transcriptional
activators, which allows transcription to be influenced by multiple
8. Some eukaryotic transcriptional activator proteins function at a
distance from the gene by binding to enhancers, causing the
formation of a loop in the DNA, which brings the promoter and
enhancer into close proximity. Some distant-acting sequences
analogous to enhancers have been described in bacterial cells,
but they appear to be less common.
9. The greater time lag between transcription and translation in
eukaryotic cells than in bacterial cells allows mRNA stability and
mRNA processing to play larger roles in eukaryotic gene regulation.
10. Regulation by siRNAs and miRNAs, which is extensive in
eukaryotes, is absent from bacterial cells.

Model Genetic Organism
The Plant Arabidopsis thaliana
Much of the early work in genetics was carried out
on plants, including Mendel’s seminal discoveries
in pea plants as well as in important aspects of
heredity, gene mapping, chromosome genetics, and quantitative inheritance in corn, wheat, beans, and other plants.

However, by the mid-twentieth century, many geneticists
had turned to bacteria, viruses, yeast, Drosophila, and mouse
genetic models. Because a good genetic plant model did not
exist, plants were relatively neglected, particularly for the
study of molecular genetic processes.
This neglect of plants changed in the last part of the
twentieth century with the widespread introduction of a new
genetic model organism, the plant Arabidopsis thaliana
(Figure 12.21). Arabidopsis thaliana was identified in the sixteenth century, and the first mutant was reported in 1873;
but this species was not commonly studied until the first
detailed genetic maps appeared in the early 1980s. Today,
Arabidopsis figures prominently in the study of genome
structure, gene regulation, development, and evolution in
plants, and it provides important basic information about
plant genetics that is applied to other economically important plant species.

Advantages of Arabidopsis as a model genetic organism
The mustard Arabidopsis thaliana is a member of the Brassicaceae family and grows as a weed in many parts of the
world. Except in its role as a model genetic organism,
Arabidopsis has no economic importance, but it has a number of characteristics that make it well suited to the study
of genetics. As an angiosperm, it has features in common
with other flowering plants, some of which play critical
roles in the ecosystem or are important sources of food,
fiber, building materials, and pharmaceuticals. Arabidopsis’s chief advantages are its small size (maximum height of
10 to 20 cm), prolific reproduction, and small genome (see
Figure 12.21).
Arabidopsis thaliana completes development—from
seed germination to seed production—in about 6 weeks. Its
small size and ability to grow under low illumination make
it ideal for laboratory culture. Each plant is capable of producing from 10,000 to 40,000 seeds, and the seeds typically
have a high rate of germination; so large numbers of progeny can be obtained from single genetic crosses.
Another key advantage for molecular studies is
Arabidopsis’s small genome, which consists of only 125
million base pairs of DNA on five pairs of chromosomes,
compared with 2.5 billion base pairs of DNA in the maize
genome and 16 billion base pairs in the wheat genome.
The genome of A. thaliana was completely sequenced in
2000, providing detailed information about gene structure
and organization in this species. A number of variants of
A. thaliana—called ecotypes—that vary in shape, size,
physiological characteristics, and DNA sequence are available for study.

Life cycle of Arabidopsis The Arabidopsis life cycle is
fairly typical of most flowering plants (see Figures 2.17 and
12.21). The main, vegetative part of the plant is diploid;
haploid gametes are produced in the pollen and ovaries.
When a pollen grain lands on the stigma of a flower, a pollen

The Plant
Arabidopsis thaliana


• Small size
• Short generation time of 6 weeks


• Each plant can produce from
10,000 to 40,000 seeds
• Ability to grow in laboratory


• Small genome for a plant

Flowering plant
10–20 cm
Roots, one primary
shoot, simple
leaves, flowers

• Many variants available
• Self-fertilizes and outcrosses




Life Cycle



Amount of DNA:


Number of genes:
Percentage of genes in
common with humans:
Average gene size:

Pollen tube
Polar nuclei


Egg cell

Genome sequenced
in year:

5 pairs (2n = 10)
125 million base
2000 base pairs

• Plant-genome organization

• Genetics of plant development

• Gene regulation

• Genetics of flowering

12.21 Arabidopsis thaliana is a model genetic organism that serves as an important
subject for research on genetic processes in plants. [Photograph courtesy of Dr. Paul Franz.]

tube grows into the pistil and ovary. Two haploid sperm
nuclei contained in each pollen grain travel down the pollen
tube and enter the embryo sac. There, one of the haploid
sperm cells fertilizes the haploid egg cell to produce a
diploid zygote. The other haploid sperm cell fuses with two
haploid nuclei to form the 3n endosperm, which provides
tissue that will nourish the growing embryonic plant. The
zygotes develop within the seeds, which are produced in a
long pod.
Under appropriate conditions, the embryo germinates
and begins to grow into a plant. The shoot grows upward and
the roots downward, a compact rosette of leaves is produced

and, under the right conditions, the shoot enlarges and differentiates into flower structures. At maturity, A. thaliana is
a low-growing plant with roots, a main shoot with branches
that bear mature leaves, and small white flowers at the tips of
the branches.

Genetic techniques with Arabidopsis A number of
traditional and modern molecular techniques are commonly used with Arabidopsis and provide it with special
advantages for genetic studies. Arabidopsis can self-fertilize,
which means that any recessive mutation appearing in the
germ line can be recovered in the immediate progeny.



Chapter 12

Cross-fertilization also is possible by removing the anther
from one plant and dusting pollen on the stigma of another
plant—essentially the same technique used by Gregor
Mendel with pea plants (see Figure 3.3).
As already mentioned, many naturally occurring variants of Arabidopsis are available for study, and new mutations can be produced by exposing its seeds to chemical
mutagens, radiation, or transposable elements that randomly insert into genes. The large number of offspring produced by Arabidopsis facilitates screening for rare mutations.
Genes from other organisms can be transferred to
Arabidopsis by means of the Ti plasmid from the bacterium
Agrobacterium tumefaciens, which naturally infects plants and
transfers the Ti plasmid to plant cells. Subsequent to the

transfer, the Ti plasmid randomly inserts into the DNA of the
plant that it infects, thereby generating mutations in the plant
DNA in a process called insertional mutagenesis. Geneticists
have modified the Ti plasmid to carry a GUS gene, which has
no promoter of its own. The GUS gene encodes an enzyme
that converts a colorless compound (X-Glu) into a blue dye.
Because the GUS gene has no promoter, it is expressed only
when inserted into the coding sequence of a plant gene. When
that happens, the enzyme encoded by GUS is synthesized and
converts X-Glu into a blue dye that stains the cell. This dye
provides a means to visually determine the expression pattern
of a gene that has been interrupted by Ti DNA, producing
information about the expression of genes that are mutated
by insertional mutagenesis. ᭿

Concepts Summary
• Gene expression can be controlled at different levels, including

the alteration of gene structure, transcription, mRNA
processing, RNA stability, translation, and posttranslational
modification. Much of gene regulation is through the action
of regulatory proteins binding to specific sequences in DNA.
Genes in bacterial cells are typically clustered into operons—
groups of functionally related structural genes and the
sequences that control their transcription. Structural genes in
an operon are transcribed together as a single mRNA molecule.
In negative control, a repressor protein binds to DNA and
inhibits transcription. In positive control, an activator protein
binds to DNA and stimulates transcription. In inducible
operons, transcription is normally off and must be turned on;
in repressible operons, transcription is normally on and must
be turned off.
The lac operon of E. coli is a negative inducible operon. In
the absence of lactose, a repressor binds to the operator
and prevents the transcription of genes that encode
␤-galactosidase, permease, and transacetylase. When lactose is
present, some of it is converted into allolactose, which binds
to the repressor and makes it inactive, allowing the structural
genes to be transcribed.
Positive control in the lac and other operons is through
catabolite repression. When complexed with cAMP, the
catabolite activator protein (CAP) binds to a site in or near
the promoter and stimulates the transcription of the structural
genes. Levels of cAMP are inversely correlated with glucose; so
low levels of glucose stimulate transcription and high levels
inhibit transcription.
The trp operon of E. coli is a negative repressible operon that
controls the biosynthesis of tryptophan.
Eukaryotic cells differ from bacteria in several ways that affect
gene regulation, including, in eukaryotes, the absence of
operons, the presence of chromatin and a nuclear membrane,
and the more common use of activators.

• In eukaryotic cells, chromatin structure represses gene
expression. In transcription, chromatin structure may be
altered by the modification of histone proteins, including
acetylation, phosphorylation, and methylation. The
repositioning of nucleosomes and the methylation of
DNA also affect transcription.

• The initiation of eukaryotic transcription is controlled by
general transcription factors that assemble into the basal
transcription apparatus and by transcriptional activator
proteins that stimulate normal levels of transcription by
binding to regulatory promoters and enhancers.

• Enhancers affect the transcription of distant genes.
Transcriptional activators bind to enhancers and interact
with the basal transcription apparatus by causing the
intervening DNA to loop out. Insulators limit the action of
enhancers by blocking their action in a position-dependent

• Coordinately controlled genes in eukaryotic cells respond to
the same factors because they have common response
elements that are stimulated by the same transcriptional

• Gene expression in eukaryotic cells can be influenced by RNA
processing and by changes in RNA stability. The 5Ј cap, the
coding sequence, the 3Ј UTR, and the poly(A) tail are
important in controlling the stability of eukaryotic mRNAs.

• RNA silencing plays an important role in eukaryotic gene regulation. Small RNA molecules (siRNAs and miRNAs) combine
with proteins and bind to sequences on mRNA or DNA. These
complexes cleave RNA, inhibit translation, affect RNA
degradation, and silence transcription.

• Control of the posttranslational modification of proteins may
play a role in gene expression.

• Arabidoposis thaliana possesses a number of characteristics
that make it an ideal model genetic organism.

Control of Gene Expression


Important Terms
gene regulation (p. 290)
structural gene (p. 291)
regulatory gene (p. 291)
constitutive gene (p. 291)
regulatory element (p. 291)
operon (p. 292)
regulator gene (p. 292)
regulator protein (p. 292)
operator (p. 292)
negative control (p. 293)
positive control (p. 293)
inducible operon (p. 293)

repressible operon (p. 293)
inducer (p. 293)
allosteric protein (p. 293)
corepressor (p. 294)
coordinate induction (p. 297)
partial diploid (p. 298)
constitutive mutation (p. 299)
catabolite repression (p. 302)
catabolite activator protein (CAP) (p. 302)
adenosine-3Ј,5Ј-cyclic monophosphate
(cAMP) (p. 302)

histone code (p. 304)
chromatin-remodeling complex (p. 306)
general transcription factor (p. 306)
transcriptional activator protein (p. 306)
enhancer (p. 306)
coactivator (p. 306)
silencer (p. 306)
insulator (p. 307)
heat-shock protein (p. 308)
response element (p. 308)

Answers to Concept Checks
1. A constitutive gene is not regulated and is expressed continually.
2. Because it is the first step in the process of information
transfer from DNA to protein. For cellular efficiency, gene
expression is often regulated early in the process of protein
3. d
4. d
5. c

6. b
7. b
8. The DNA between the enhancer and the promoter loops out,
and so transcription activators bound to the enhancer are able to
interact directly with the transcription apparatus.
9. The poly(A) tail stabilizes the 5Ј cap, which must be removed
before the mRNA molecule can be degraded from the 5Ј end.
10. d

Worked Problems
1. A regulator gene produces a repressor in an inducible operon.
A geneticist isolates several constitutive mutations affecting this
operon. Where might these constitutive mutations occur? How
would the mutations cause the operon to be constitutive?

• Solution
An inducible operon is normally not being transcribed, meaning
that the repressor is active and binds to the operator, inhibiting
transcription. Transcription takes place when the inducer binds
to the repressor, making it unable to bind to the operator.
Constitutive mutations cause transcription to take place at all
times, whether the inducer is present or not. Constitutive
mutations might occur in the regulator gene, altering the
repressor so that it is never able to bind to the operator.
Alternatively, constitutive mutations might occur in the
operator, altering the binding site for the repressor so that
the repressor is unable to bind under any conditions.
2. The fox operon, which has sequences A, B, C, and D (which
may represent either structural genes or regulatory sequences),
encodes enzymes 1 and 2. Mutations in sequences A, B, C, and D
have the following effects, where a plus sign (ϩ) indicates that the
enzyme is synthesized and a minus sign (Ϫ) indicates that the
enzyme is not synthesized.

in sequence
No mutation

Fox absent


Fox present


a. Is the fox operon inducible or repressible?
b. Indicate which sequence (A, B, C, or D) is part of the
following components of the operon:
Regulator gene




Structural gene for enzyme 1


Structural gene for enzyme 2


• Solution
Because the structural genes in an operon are coordinately
expressed, mutations that affect only one enzyme are likely to