Cell and Molecular
Biology
Ninth Edition

Gerald Karp, Janet Iwasa, Wallace Marshall

Chapter 12
Control of Gene Expression

12.1 | Control of Gene Expression in Bacteria
(1 of 10)
 Cells possess mechanisms that allow them to precisely regulate
their genetic information, expressing genes only when they are
needed.
 Gene expression changes are seen in many diseases,

• Cancer
• 10 percent of all prescribed drugs, including steroid hormone analogs, act
at the level of gene expression.

 New technologies allow sequencing of entire genomes
• Gene regulation and coordination insights

Copyright © 2020 John Wiley & Sons, Inc.

12.1 | Control of Gene Expression in Bacteria
(2 of 10)
Organization of Bacterial Genomes
 Prokaryotic genomes – circular, double-stranded
 Nearly all the DNA encodes RNAs or proteins
 Genes involved in the same biological process are often grouped
together to allow coordinate regulation of the entire group
 Because of this arrangement, the start and stop of transcription and
translation are precisely regulated.

Copyright © 2020 John Wiley & Sons, Inc.

12.1 | Control of Gene Expression in Bacteria
(3 of 10)
The Bacterial Operon
 Bacterial cells selectively express
genes to use available resources
efficiently
 Operons to be considered control:
• Use of the sugar lactose via βgalactosidase synthesis
• Regulation of tryptophan levels
via repression of the genes that
encode enzymes for tryptophan
synthesis.

Fig. 12.1 The kinetics of β-galactosidase
induction in E. coli
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12.1 | Control of Gene Expression in Bacteria
(4 of 10)
The Bacterial Operon
 An operon is a functional
complex of genes containing
the information for enzymes
of a metabolic pathway.
 It includes:
1. Structural genes – code for
the enzymes
2. Promoter – where the RNA
polymerase binds.
3. Operator – site next to
promoter where the
regulatory protein can bind.

Fig. 12.2 Organization of a bacterial operon

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12.1 | Control of Gene Expression in Bacteria
(5 of 10)
The Bacterial Operon
4. repressor which binds to a
specific DNA sequence to
determine whether or not a
particular gene is transcribed.
RNA polymerase is unable to
bind to the promoter if the
repressor is bound.
5. regulatory gene encodes the
repressor protein.
Fig. 12.2 Organization of a bacterial operon

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12.1 | Control of Gene Expression in Bacteria
(6 of 10)
The Bacterial Operon: The Trp Operon
 In a repressible operon, the repressor
cannot bind to the operator DNA unless
it is complexed with a specific factor that
functions as a corepressor.
 Absence of tryptophan → RNA
polymerase binds to the promoter and
transcribes genes of the trp operon.
 Increased concentrations of tryptophan
leads to the formation of the
tryptophan–repressor complex → binds
to the operator and blocks transcription
Fig. 12.3a Gene regulation by operons
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12.1 | Control of Gene Expression in Bacteria
(7 of 10)
The Bacterial Operon: The Lac Operon
 The lac operon is an inducible
operon, which is turned on in the
presence of lactose (inducer).
 Lactose binds to the repressor,
changing its conformation and
making it unable to bind to the
operator.
 A repressor protein can bind to the
operator and prevent transcription in
the absence of lactose.
Fig. 12.3b Gene regulation by operons
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12.1 | Control of Gene Expression in Bacteria
(8 of 10)
The Bacterial Operon: Catabolite Repression
 The lac operon is also under catabolite repression, expressed at highest
levels when lactose is present and glucose concentration is low.
 The lac repressor exerts negative control. The glucose effect is an
example of positive control.

Fig. 12.4 Nucleotide sequence of the control regions of the lac operon
Copyright © 2020 John Wiley & Sons, Inc.

12.1 | Control of Gene Expression in Bacteria
(9 of 10)
The Bacterial Operon: Attenuation
 For the trp operon, a second form of feedback regulation controls
transcription termination, a mechanism referred to as attenuation.
 The mechanism of attenuation links alternative RNA secondary
structures to transcription termination.
 The decision for transcription termination is regulated by the
concentration of tryptophan.

Copyright © 2020 John Wiley & Sons, Inc.

12.1 | Control of Gene Expression in Bacteria
(10 of 10)
Riboswitches
 Bacterial mRNAs can bind to a small metabolite in their 5' untranslated
region, which in turn alters the gene involved in the production of such
metabolite.
 These mRNAs are called riboswitches because they undergo a
conformational change and can suppress gene expression.
 Most riboswitches suppress gene expression by blocking either
termination of transcription or initiation of translation.
 Riboswitches allow bacteria to regulate gene expression in response to
some metabolites.

Copyright © 2020 John Wiley & Sons, Inc.

12.2 | Engineering Linkage: Building Digital Logic
with Genes
 Cellular engineering provides approaches for reprogramming cell
behavior
 Ligand binding to gene control elements regulated by
positive/negative control elements can permit construction of
logic gate equivalents
 Experiments modifying existing promoters show that
transcriptional regulation can be harnessed to build digital logic
inside a cell
 Future potential for therapeutics in cancer treatment

Copyright © 2020 John Wiley & Sons, Inc.

12.3 | Structure of the Nuclear Envelope (1 of 7)
 A typical eukaryotic non-dividing nucleus in housed by an envelope and
contains:
•
•
•
•

Chromosomes as extended fibers of chromatin.
Nucleoli for rRNA synthesis.
Nucleoplasm as the fluid where solutes are dissolved.
The nuclear matrix, which is the protein-containing fibrillar network.

Fig. 12.6 The cell nucleus
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12.3 | Structure of the Nuclear Envelope (2 of 7)
 Two membranes separated by a nuclear space.
 Membranes are fused at sites forming nuclear pores.
 Inner surface of the nuclear envelope is lined by the nuclear lamina.
 Contains around 60 distinct transmembrane proteins.

Fig. 12.7 The nuclear envelope
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12.3 | Structure of the Nuclear Envelope (3 of 7)
 The nuclear lamina supports the nuclear envelope and is composed of
lamins.
 Its integrity is regulated by phosphorylation/dephosphorylation of
intermediate filaments.

Fig. 12.8 The nuclear lamina
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12.3 | Structure of the Nuclear Envelope (4 of 7)
The Nuclear Pore Complex and Its Role in Nucleocytoplasmic Trafficking

 The nuclear envelope is the barrier
between the nucleus and
cytoplasm, and nuclear pores are
the gateways.

• proteins synthesized in the
cytoplasm and transported across
the nuclear envelope
• mRNAs, tRNAs, and ribosomal
subunits are manufactured in the
nucleus and transported to the
cytoplasm

Fig. 12.9 Movement of materials
through the nuclear pore
Copyright © 2020 John Wiley & Sons, Inc.

12.3 | Structure of the Nuclear Envelope (5 of 7)
The Nuclear Pore Complex and Its Role in Nucleocytoplasmic Trafficking

 Doughnut-shaped structure
called that straddles the nuclear
envelope, projecting into both
the cytoplasm and nucleoplasm.
 Composed of ~30 proteins
called nucleoporins.
 Huge complex (15–30X mass of
a ribosome) that exhibits
octagonal symmetry.
 The NPC is not static, as many of
its proteins are replaced over a
period of seconds to minutes.

Fig. 12.11 Model
of a vertebrate
nuclear pore
complex (NPC)

Fig. 12.10 Scanning
electron micrographs
of the NPC from an
amphibian oocyte

Copyright © 2020 John Wiley & Sons, Inc.

12.3 | Structure of the Nuclear Envelope (6 of 7)
The Nuclear Pore Complex and Its Role in Nucleocytoplasmic Trafficking

 Cytoplasmic proteins are
targeted for the nucleus by the
nuclear localization signal (NLS).
 Transport receptors include:

• importins to move molecules
from the cytoplasm into the
nucleus
• exportins to move molecules in
the opposite direction.

Fig. 12.12 Importing proteins from the
cytoplasm into the nucleus
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12.3 | Structure of the Nuclear Envelope (7 of 7)
RNA Transport
 mRNAs, rRNAs, snoRNAs, miRNAs, and tRNAs are synthesized in the
nucleus and function in the cytoplasm or are modified in the cytoplasm
and return to function in the nucleus.
 These RNAs move through the NPC as ribonucleoproteins (RNPs).
 Only mature, fully processed mRNAs are capable of nuclear export, as an
mRNA with an unspliced intron is retained in the nucleus.

Copyright © 2020 John Wiley & Sons, Inc.

12.4 | Chromosomes and Chromatin (1 of 20)
Nucleosomes: The Lowest Level of Chromosome Organization
 Each chromosome contains a
single, continuous DNA molecule.
 Chromosomes consist of:
• chromatin fibers, composed of
DNA and associated proteins
• histones, a group of highly
conserved proteins
• DNA and histones are organized
into repeating subunits called
nucleosomes.

Fig. 12.13 Nucleosomal organization
of chromatin
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12.4 | Chromosomes and Chromatin (2 of 20)
Nucleosomes: The Lowest Level of Chromosome Organization
 Histone H1 serves as a linker.
 DNA is wrapped around the core
complex.
 Complex consists of two (H2A,
H2B, H3, H4) forming an octamer.
 Histone modification is one
mechanism to alter the character
of nucleosomes.
 Histones, regulatory proteins, and
enzymes dynamically mediate
DNA transcription, compaction,
replication, recombination, and
repair.

Fig. 12.14 The structure of a nucleosome

Copyright © 2020 John Wiley & Sons, Inc.

12.4 | Chromosomes and Chromatin (3 of 20)
Higher Levels of Chromatin Structure
 30-nm chromatin fiber
 Gathered into a series of large,
supercoiled loops, or domains,
compacted into thicker (80–100
nm) fibers.
 DNA loops are tethered at their
bases to proteins that may be
part of a poorly defined nuclear
scaffold.
 Cohesin, best known for holding
replicated DNA molecules
together during mitosis
maintains these DNA loops.

12.16 Chromatin loops: a higher level of
chromatin structure

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12.4 | Chromosomes and Chromatin (4 of 20)
Higher Levels of Chromatin Structure
 1 um mitotic chromosome length
contains 1 cm DNA length
 10,000:1 packing ratio
 Incompletely understood process

Fig. 12.17 Levels of
organization of chromatin
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12.4 | Chromosomes and Chromatin (5 of 20)
Heterochromatin
 After mitosis has been completed, most of the chromatin in highly
compacted mitotic chromosomes returns to its diffuse interphase
condition.
 Euchromatin returns to a dispersed state after mitosis, heterochromatin
is condensed during interphase.
 Constitutive heterochromatin remains condensed all the time. It is
found mostly around centromeres and telomeres and consists of highly
repeated sequences and few genes.
 Facultative heterochromatin is inactivated during certain phases of the
organism's life. It is found in one of the X chromosomes as a Barr body
through X inactivation, a random process that makes adult females
genetic mosaics.

Copyright © 2020 John Wiley & Sons, Inc.

12.4 | Chromosomes and Chromatin (6 of 20)
Heterochromatin
 Although cells of females contain two X chromosomes, only one of them
is transcriptionally active. The other X chromosome remains condensed
as a heterochromatic clump called a Barr body.

Fig. 12.18 Facultative heterochromatin: the inactive X chromosome
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12.4 | Chromosomes and Chromatin (7 of 20)
X Chromosome Inactivation (Heterochromatization)
 X chromosome affected in female mammals occurs during early
embryonic development and leads to the inactivation of the genes on
that chromosome.
 Random process – paternally or maternally derived X chromosome stand
an equal chance of becoming inactivated in any given cell.
 Reactivation of the heterochromatinized X chromosome occurs in female
germ cells prior to the onset of meiosis.

Copyright © 2020 John Wiley & Sons, Inc.

12.4 | Chromosomes and Chromatin (8 of 20)
The Histone Code and Formation of Heterochromatin
 The histone code
hypothesis states that the
activity of a chromatin
region depends on the
degree of chemical
modification of histone tails.
 Histone tail modifications
can:
1. Serve as docking sites to
recruit nonhistone proteins.
2. Alter the way histones of
neighboring nucleosomes
interact.

Fig. 12.19 Histone modification at the histone

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12.4 | Chromosomes and Chromatin (9 of 20)
The Histone Code and Formation of Heterochromatin
 The majority of modified amino acids reside on the N-termini of H3 and
H4.
 Each of the bound proteins possesses an activity that alters the structure
and/or function of the chromatin.
 Heterochromatin has many methylated H3 histones, which stabilize the
compact nature of the chromatin.

Fig. 12.20 Examples of proteins that bind selectively to modified H3 or H4 residues
Copyright © 2020 John Wiley & Sons, Inc.

12.4 | Chromosomes and Chromatin (10 of 20)
The Histone Code and Formation of Heterochromatin
 Removal of the acetyl groups
from H3 and H4 histones is
among the initial steps in
conversion of euchromatin into
heterochromatin.
 Inactive, heterochromatic X
chromosome → deacetylated
histones.
 Active, euchromatic X
chromosome → normal level of
acetylation.

Fig. 12.21 Experimental demonstration of a
correlation between transcriptional activity
and histone acetylation

Copyright © 2020 John Wiley & Sons, Inc.

12.4 | Chromosomes and Chromatin (11 of 20)
The Histone Code and Formation of
Heterochromatin
1. Histone deacetylation is
accompanied by methylation of
H3K9 histone methyltransferase
2. Methylated H3K9 binds to
proteins with a chromodomain
like heterochromatic protein 1
(HP1).
3. Once HP1 is bound to the histone
tails, HP1-HP1 interactions
facilitate chromatin packaging into
a heterochromatin state.
 This process can be driven by small
RNAs.

Fig. 12.22 A model in which small RNAs
govern the formation of heterochromatin

Copyright © 2020 John Wiley & Sons, Inc.

12.4 | Chromosomes and Chromatin (12 of 20)
The Structure of a Mitotic Chromosome
 Highly condensed chromatin in mitotic
cells
 During mitotic prophase, chromosomes
adopt a distinct shape determined by the
length of the DNA molecule and the
position of the centromere.
 Techniques can be used to visualize the
DNA.

Fig. 12.23a Human mitotic
chromosomes and karyotypes
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12.4 | Chromosomes and Chromatin (13 of 20)
The Structure of a Mitotic Chromosome
 Chromosome can be labeled with
multicolored, fluorescent DNA
probes that bind specifically to
particular chromosomes.
 A karyotype is a preparation of
homologous pairs ordered
according to size.
 The pattern on a karyotype may
be used to screen chromosomal
abnormalities.

Fig. 12.23b,c Human mitotic
chromosomes and karyotypes
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12.4 | Chromosomes and Chromatin (14 of 20)
Telomeres
 Each eukaryotic chromosome
contains a single, continuous DNA
molecule.
 DNA tips have repeated sequences
that, together with a group of
specialized proteins, form a cap
called a telomere.
 The same telomere sequence is
found throughout vertebrates, and
similar sequences are found in most
other organisms.
Fig. 12.24 Telomeres
Copyright © 2020 John Wiley & Sons, Inc.

12.4 | Chromosomes and Chromatin (15 of 20)
Telomeres
 The 5' end ends of the newly
synthesized strands contain a short
segment of RNA
 RNA primer removal causes 5' DNA end
to be shorter relative to the previous
generation
 If cells were not able to replicate the
ends of their DNA, the chromosomes
would become shorter and shorter with
each round of cell division, called the
“end-replication problem.”
Fig. 12.25a,b The end-replication
problem and the role of telomerase
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12.4 | Chromosomes and Chromatin (16 of 20)
Telomeres
 New repeats are added by a
telomerase, a reverse
transcriptase that synthesizes
DNA from a DNA template.
 Unlike most reverse
transcriptases, the enzyme itself
contains the RNA that serves as
its template.
 Once the 3' end of the strand has
been lengthened, a conventional
DNA polymerase can return the
5' end of the complementary
strand to its previous length.

Fig. 12.25c The end-replication problem
and the role of telomerase

Copyright © 2020 John Wiley & Sons, Inc.

12.4 | Chromosomes and Chromatin (17 of 20)
Telomeres
 Telomere significance:

• They are required for the
complete replication of the
chromosome;
• They form caps that protect the
chromosomes from nucleases
and other destabilizing
influences;
• They prevent the ends of
chromosomes from fusing with
one another.

Fig. 12.26 Telomerase and chromosome
integrity
Copyright © 2020 John Wiley & Sons, Inc.

12.4 | Chromosomes and Chromatin (18 of 20)
Telomeres
 In somatic cells, telomere lengths are reduced each cell division to limit
cell doublings.
 A critical point occurs from telomere shortening when cells stop their
growth and division.
 In contrast, cells that are able to resume telomerase expression continue
to proliferate.
 These cells continue to divide and do not shown normal signs of aging.
 Approximately 90% of human tumors have cells with active telomerase.

Copyright © 2020 John Wiley & Sons, Inc.

12.4 | Chromosomes and Chromatin (19 of 20)
Centromeres
 The centromere is located at markedly indented chromosomal site
 Tandemly repeated constitutive heterochromatin.
 Centromeric DNA is the site of microtubule attachment during mitosis via
CENP-A H3 variant.

Fig. 12.27 Each mitotic chromosome has a centromere with a site marked by a distinct
indentation
Copyright © 2020 John Wiley & Sons, Inc.

12.4 | Chromosomes and Chromatin (20 of 20)
Epigenetics: There's More to Inheritance than DNA
 Epigenetic inheritance depends on factors other than DNA sequences.
 X-chromosome inactivation is an example, since the two X chromosomes
can have identical DNA sequences, but one is inactivated and the other is
not.
 An epigenetic state can usually be reversed; X chromosomes, for
example, are reactivated prior to formation of gametes.
 Differences in disease susceptibility and longevity between genetically
identical twins may be due, in part, to epigenetic differences that appear
between the twins as they age.

Copyright © 2020 John Wiley & Sons, Inc.

12.5 | The Nucleus as an Organized Organelle
(1 of 5)
 Chromatin fibers of an
interphase chromosome are are
concentrated into distinct
territories.
 A difference in nuclear location
may be related to the levels of
activity of chromosomes.
 Chromosome number 18 is
relatively devoid of genes,
whereas chromosome number
19 is rich in protein-coding
sequences, many of which are
presumably transcribed.

Fig. 12.28 Chromosome territories

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Fig. 12.29 Localizing
specific chromosomes
within an interphase
nucleus

12.5 | The Nucleus as an Organized Organelle
(2 of 5)
 Interchromosomal interactions can be shown through hormone
treatment.
 In response to estrogen, two target genes in humans are
repositioned into close physical proximity to one another, and the
two gene loci become co-localized on the periphery of their
territories.
 Genes are physically moved to sites within the nucleus called
transcription factories, where the transcription machinery is
concentrated, and genes involved in the same response tend to
become co-localized in the same factory.

Copyright © 2020 John Wiley & Sons, Inc.

12.5 | The Nucleus as an Organized Organelle
(3 of 5)

Fig. 12.30 Interactions can occur between distantly located genes in response to
physiological stimuli
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12.5 | The Nucleus as an Organized Organelle
(4 of 5)
 The genome is packed into a
series of regions where DNA
within such a region tends to
interact much more strongly
with other DNA in the same
region than it does with other
parts of the genome.
 These regions are known as
topologically associated
domains (TADs).

Fig. 12.31 Global packing of the genome
within the nucleus
Copyright © 2020 John Wiley & Sons, Inc.

12.5 | The Nucleus as an Organized Organelle
(5 of 5)
 The processing machinery is concentrated within irregular domains,
referred to as “speckles.”
 Speckles function as dynamic storage depots that supply splicing factors
for use at nearby sites of transcription.

Fig. 12.32 Nuclear compartmentalization of the cell's mRNA processing machinery
Copyright © 2020 John Wiley & Sons, Inc.

12.6 | An Overview of Gene Regulation in
Eukaryotes (1 of 2)
 Differentiated cells retain a full
set of genes.
 Nuclei from cells of adult animals
are capable of supporting the
development of a new
individual, as demonstrated in
experiments.
 From cloning experiments, a
nucleus from a differentiated cell
can be reprogrammed by factors
that reside in the cytoplasm of its
new environment.

Fig. 12.33 The cloning of animals
demonstrates that nuclei retain a
complete set of genetic information

Copyright © 2020 John Wiley & Sons, Inc.

12.6 | An Overview of Gene Regulation in
Eukaryotes (2 of 2)
 Genes are turned on and off as a
result of interaction with
regulatory proteins.
 Each cell type contains a unique
set of proteins.
 Regulation of gene expression
occurs on four levels:
1.
2.
3.
4.

Transcriptional control
Processing control
Translational control
Posttranslational control
Fig. 12.34 Eukaryotic gene regulation
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12.7 | Transcriptional Control (1 of 27)
 Differential transcription is the
mechanism by which eukaryotic
cells determine which proteins
are synthesized.
 Differential gene expression is
found in various conditions:
1. Cells at different stages of
embryonic development
2. Cells in different tissues
3. Cells that are exposed to
different types of stimuli
Fig. 12.35 Experimental demonstration of
the tissue-specific gene

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12.7 | Transcriptional Control (2 of 27)
DNA Microarrays
 DNA microarrays can monitor the
expression of thousands of genes
simultaneously.
 Immobilized fragments of DNA are
hybridized with fluorescent cDNAs.
 Genes that are expressed show up
as fluorescent spots on
immobilized genes.

Fig. 12.36a DNA microarrays
and analysis of gene expression
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12.7 | Transcriptional Control (3 of 27)
DNA Microarrays
 DNA microarrays are used to study changes in gene expression that occur
during events like cell division and the transformation of a normal cell
into a malignant cell.
 It is possible to study the diversity of RNAs being produced by a single
tumor cell, once the cDNAs are amplified by PCR.

Fig. 12.36b–d DNA microarrays and analysis of gene expression
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12.7 | Transcriptional Control (4 of 27)
RNA Sequencing
 DNA microarrays and RNA
sequencing (RNA-Seq) of small
fragments of cDNAs derived from
RNA can facilitate the diagnosis
and treatment of human
diseases.
 Personalized medicine in the
future will be reliant upon
transcription profiling for
diagnosis, treatment plan, and
monitoring the effectiveness of
the treatment.
Fig. 12.37 Transcription profiling to
personalize breast cancer therapy
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