Rajiv Gandhi University of Health Sciences

Access Provided by:

Harper's Illustrated Biochemistry, 32nd Edition

Chapter 38: Regulation of Gene Expression

P. Anthony Weil

OBJECTIVES

OBJECTIVES

After studying this chapter, you should be able to:

Explain that the many steps involved in the vectorial processes of gene expression: targeted modulation of gene copy number, gene
rearrangement, transcription, mRNA processing and transport from the nucleus, translation, protein subcellular compartmentalization,
posttranslational modification, and degradation are all subject to regulatory control, both positive and negative. Changes in any, or multiple of
these processes, can increase or decrease the amount and/or activity of the cognate gene product.

Appreciate that DNA­binding transcription factors, proteins that bind to specific DNA sequences that are physically linked to their target
transcriptional promoter elements, can either activate or repress gene transcription.

Recognize that DNA­binding transcription factors are often modular proteins composed of structurally and functionally distinct domains.
These transcription factors can directly or indirectly control messenger RNA (mRNA) gene transcription, either through contacts with RNA
polymerase and its cofactors, or through interactions with coregulators that modulate nucleosome occupancy, position, structure,
composition, and histone covalent modifications.

Understand that nucleosome­directed regulatory events typically increase or decrease the accessibility of the underlying DNA such as enhancer
or promoter sequences, although some nucleosome modifications can also create new binding sites for other coregulators.

Describe how the processes of gene transcription, RNA processing, and nuclear export of RNA are all coupled.

Describe the phenomenon of epigenetic gene regulation and how such processes occur at the molecular level.

BIOMEDICAL IMPORTANCE
Organisms alter expression of genes in response to genetic developmental cues or programs, environmental challenges, or disease, by modulating the
amount, the spatial, and/or the temporal patterns of gene expression. The mechanisms controlling gene expression have been studied in detail and
often involve changes in gene transcription. Control of transcription ultimately results from changes in the mode of interaction of specific regulatory
molecules, usually proteins, with various regions of DNA in the regulated gene. Such interactions can either have a positive or negative effect on
transcription. Transcription control can result in tissue­specific gene expression, and gene regulation can be influenced by a range of physiologic,
biologic, environmental, and pharmacologic agents.

In addition to transcription level controls, gene expression can also be modulated by gene amplification, gene rearrangement, posttranscriptional
modifications, RNA stabilization, translational control, protein modification, protein compartmentalization, and protein stabilization or degradation.
Many of the mechanisms that control gene expression are utilized to respond to developmental cues, growth factors, hormones, environmental
agents, and therapeutic drugs. Dysregulation of gene expression can lead to human disease. Thus, a molecular understanding of these processes will
lead to development of therapeutics that can alter pathophysiologic mechanisms or inhibit the function or arrest the growth of pathogenic organisms.

REGULATED EXPRESSION OF GENES IS REQUIRED FOR DEVELOPMENT, DIFFERENTIATION, &

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186
ADAPTATION
Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 1 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
The genetic information present in each normal somatic cell of a metazoan organism is practically identical. The genetically reproducible, hardwired
exceptions are found in those few cells that have amplified or rearranged genes in order to perform specialized cellular functions. Of course, in various
modifications, RNA stabilization, translational control, protein modification, protein compartmentalization, and protein stabilization or degradation.
Rajiv Gandhi University of Health Sciences
Many of the mechanisms that control gene expression are utilized to respond to developmental cues, growth factors, hormones, environmental
Access Provided by:
agents, and therapeutic drugs. Dysregulation of gene expression can lead to human disease. Thus, a molecular understanding of these processes will
lead to development of therapeutics that can alter pathophysiologic mechanisms or inhibit the function or arrest the growth of pathogenic organisms.

REGULATED EXPRESSION OF GENES IS REQUIRED FOR DEVELOPMENT, DIFFERENTIATION, &

ADAPTATION
The genetic information present in each normal somatic cell of a metazoan organism is practically identical. The genetically reproducible, hardwired
exceptions are found in those few cells that have amplified or rearranged genes in order to perform specialized cellular functions. Of course, in various
disease states chromosome integrity is altered (ie, cancer; see Figure 56–11) sometimes even at the whole chromosome level (eg, trisomy 21, that
causes Down syndrome). Expression of the genetic information must be regulated during ontogeny and differentiation of the organism and its cellular
components. Furthermore, in order for the organism to adapt to its environment and to conserve energy and nutrients, the expression of genetic
information must be cued to extrinsic signals and respond only when necessary. As organisms have evolved, more sophisticated regulatory
mechanisms have appeared which provide the organism and its cells with the responsiveness necessary for survival in a complex environment.
Mammalian cells possess about 1000 times more genetic information than does the bacterium Escherichia coli. Much of this additional genetic
information is likely involved in regulation of gene expression during the differentiation of tissues and biologic processes in the multicellular organism
and in ensuring that the organism can respond to complex environmental challenges.

In simple terms, there are only two types of gene regulation: positive regulation and negative regulation (Table 38–1). When the expression of
genetic information is quantitatively increased by the presence of a specific regulatory element, regulation is said to be positive; when the expression
of genetic information is diminished by the presence of a specific regulatory element, regulation is said to be negative. The element or molecule
mediating negative regulation is said to be a negative regulator, a silencer or repressor; while the element mediating positive regulation is a
positive regulator, an enhancer or activator. However, a double negative has the effect of acting as a positive. Thus, an effector that inhibits the
function of a negative regulator will appear to bring about a positive regulation. Many regulated systems that appear to be induced are in fact
derepressed at the molecular level. (See Chapter 9 for additional discussion of these terms.)

TABLE 38–1
Effects of Positive & Negative Regulation on Gene Expression

Rate of Gene Expression

Negative Regulation Positive Regulation

Regulator present Decreased Increased

Regulator absent Increased Decreased

BIOLOGIC SYSTEMS EXHIBIT THREE TYPES OF TEMPORAL RESPONSES TO A REGULATORY

SIGNAL
Figure 38–1 depicts the extent or amount of gene expression in three types of temporal responses to an inducing signal. A type A response is
characterized by an increased extent of gene expression that is dependent on the continued presence of the inducing signal. When the inducing signal
is removed, the amount of gene expression diminishes to its basal level, but the amount repeatedly increases in response to the reappearance of the
specific signal. This type of response is commonly observed in prokaryotes in response to sudden changes of the intracellular concentration of a
nutrient. It is also observed in many higher organisms after exposure to inducers such as hormones, nutrients, or growth factors (see Chapter 42).

FIGURE 38–1

Diagrammatic representations of the responses of the extent of expression of a gene to specific regulatory signals as a function of
time.

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186

Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 2 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
FIGURE 38–1
Rajiv Gandhi University of Health Sciences
Access Provided by:
Diagrammatic representations of the responses of the extent of expression of a gene to specific regulatory signals as a function of
time.

A type B response exhibits an increased amount of gene expression that is transient even in the continued presence of the regulatory signal. After
the regulatory signal has terminated and the cell has been allowed to recover, a second transient response to a subsequent regulatory signal may be
observed. This phenomenon of response­desensitization recovery characterizes the action of many pharmacologic agents, but it is also a feature of
many naturally occurring processes. This type of response commonly occurs during development of an organism, when only the transient appearance
of a specific gene product is required although the signal persists.

The type C response pattern exhibits, in response to the regulatory signal, an increased extent of gene expression that persists indefinitely even after
termination of the signal. The signal acts as a trigger in this pattern. Once expression of the gene is initiated in the cell, it cannot be terminated even in
the daughter cells; it is therefore an irreversible and inherited alteration. This type of response typically occurs during the development of
differentiated function in a tissue or organ.

Simple Unicellular & Multicellular Organisms Serve as Valuable Models for the Study of Gene Expression in
Human Cells

Analysis of the regulation of gene expression in prokaryotic cells helped establish the principle that information flows from the gene to a messenger
RNA to a specific protein molecule. These studies were aided by the advanced genetic analyses that could be performed in prokaryotic and lower
eukaryotic organisms such as the baker’s yeast, Saccharomyces cerevisiae, and the fruit fly, Drosophila melanogaster, among others. In recent years,
the principles established in these studies, coupled with a variety of physical, optical, biochemical, informatic, and molecular biological techniques,
Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186
have led 38:
Chapter to remarkable
Regulationprogress
of Gene in the analysis
Expression, P.ofAnthony
gene regulation
Weil in higher eukaryotic organisms, including humans. In this chapter, the initial
Page 3 / 33
discussion
©2025 will center
McGraw onRights
Hill. All prokaryotic systems.
Reserved. The impressive
Terms genetic
of Use • Privacy studies
Policy will not
• Notice be described, but the physiology of gene expression will be
• Accessibility
discussed. However, nearly all of the conclusions about this physiology have been derived from genetic studies and confirmed by molecular biological
and biochemical experiments.
Human Cells
Rajiv Gandhi University of Health Sciences
Analysis of the regulation of gene expression in prokaryotic cells helped establish the principle that information
Access flows
Providedfrom
by: the gene to a messenger
RNA to a specific protein molecule. These studies were aided by the advanced genetic analyses that could be performed in prokaryotic and lower
eukaryotic organisms such as the baker’s yeast, Saccharomyces cerevisiae, and the fruit fly, Drosophila melanogaster, among others. In recent years,
the principles established in these studies, coupled with a variety of physical, optical, biochemical, informatic, and molecular biological techniques,
have led to remarkable progress in the analysis of gene regulation in higher eukaryotic organisms, including humans. In this chapter, the initial
discussion will center on prokaryotic systems. The impressive genetic studies will not be described, but the physiology of gene expression will be
discussed. However, nearly all of the conclusions about this physiology have been derived from genetic studies and confirmed by molecular biological
and biochemical experiments.

Some Features of Prokaryotic Gene Expression Are Unique

Before the physiology of gene expression can be explained, a few specialized genetic and regulatory terms must be defined for prokaryotic systems. In
prokaryotes, the genes involved in a metabolic pathway are often present in a linear array called an operon, for example, the lac operon. An operon
can be regulated by a single promoter or regulatory region. The cistron is the smallest unit of genetic expression. A single mRNA that encodes more
than one separately translated protein is referred to as a polycistronic mRNA. For example, the polycistronic lac operon mRNA is translated into
three separate proteins (see following discussion). Operons and polycistronic mRNAs are common in bacteria but not in eukaryotes.

An inducible gene is one whose expression increases in response to an inducer or activator, a specific positive regulatory signal. In general,
inducible genes have relatively low basal rates of transcription. By contrast, genes with high basal rates of transcription are often subject to
downregulation by repressors.

The expression of some genes is constitutive, meaning that they are expressed at a reasonably constant rate and not known to be subject to
extensive regulation. Such genes are often referred to as housekeeping genes. As a result of mutation, some inducible gene products become
constitutively expressed. A mutation resulting in constitutive expression of what was formerly a regulated gene is called a constitutive mutation.

Analysis of Lactose Metabolism in E. coli Led to the Discovery of the Basic Principles of Gene Transcription
Activation & Repression

Jacob and Monod in 1961 described their operon model in a classic paper. Their hypothesis was to a large extent based on observations on the
regulation of lactose metabolism by the intestinal bacterium E. coli. The molecular mechanisms responsible for the regulation of the genes involved in
the metabolism of lactose are now among the best­understood in any organism. β­Galactosidase hydrolyzes the β­galactoside lactose to galactose and
glucose. The gene encoding β­galactosidase (lacZ) is clustered with the genes encoding lactose permease (lacY) and thiogalactoside transacetylase
(lacA). The genes encoding these three enzymes, along with the lac promoter and lac operator (a regulatory region), and the lacI gene encoding the
LacI repressor are physically linked and constitute the lac operon as depicted in Figure 38–2. This genetic arrangement of the lac operon allows for
coordinate expression of the three enzymes concerned with lactose metabolism. Each of the linked operon genes is transcribed into one large
polycistronic mRNA molecule that contains multiple independent translation start (AUG) and stop (UAA) codons for each of the three cistrons. Thus,
each protein is translated separately, and they are not processed from a single large precursor protein.

FIGURE 38–2

The positional relationships of the protein coding and regulatory elements of the ~6kbp lac operon. lacZ encodes β­galactosidase, lacY
encodes a permease, and lacA encodes a transacetylase. lacI encodes the lac operon repressor protein. Also shown is the transcription start site for lac
operon transcription (TSS). Note that the binding site for the LacI protein (ie, lac repressor)—the lac operator (Operator)—overlaps the lac promoter.
Immediately upstream of the lac operon promoter is the binding site (CRE) for the cAMP­binding protein, CAP, the positive regulator of lac operon
transcription. See Figure 38–3 for more detail.

It is now conventional to consider that a gene includes regulatory sequences as well as the region that encodes the primary transcript. Although there
are many historical exceptions, a gene is generally italicized in lower case and the encoded protein, when abbreviated, is expressed in roman type with
the first letter capitalized. For example, the gene lacI encodes the repressor protein LacI. When E. coli is presented with lactose or some specific lactose
Downloaded
analogs under2025­5­17
appropriate3:44 P Your IP isconditions
nonrepressing 13.233.228.186
(eg, high concentrations of lactose, no or very low glucose in media; see following discussion),
Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 4 / 33
the expression
©2025 McGrawofHill.
the All
activities
Rightsof β­galactosidase,
Reserved. Termsgalactoside permease,
of Use • Privacy Policyand thiogalactoside
• Notice transacetylase is increased 100­fold to 1000­fold. This is
• Accessibility
a type A response, as depicted in Figure 38–1. The kinetics of induction can be quite rapid; lac­specific mRNAs are fully induced within ~5 minutes after
addition of lactose to a culture; β­galactosidase protein is maximal within 10 minutes. Under fully induced conditions, there can be up to 5000 β­
Rajiv Gandhi University of Health Sciences
Access Provided by:

It is now conventional to consider that a gene includes regulatory sequences as well as the region that encodes the primary transcript. Although there
are many historical exceptions, a gene is generally italicized in lower case and the encoded protein, when abbreviated, is expressed in roman type with
the first letter capitalized. For example, the gene lacI encodes the repressor protein LacI. When E. coli is presented with lactose or some specific lactose
analogs under appropriate nonrepressing conditions (eg, high concentrations of lactose, no or very low glucose in media; see following discussion),
the expression of the activities of β­galactosidase, galactoside permease, and thiogalactoside transacetylase is increased 100­fold to 1000­fold. This is
a type A response, as depicted in Figure 38–1. The kinetics of induction can be quite rapid; lac­specific mRNAs are fully induced within ~5 minutes after
addition of lactose to a culture; β­galactosidase protein is maximal within 10 minutes. Under fully induced conditions, there can be up to 5000 β­
galactosidase molecules per cell, an amount about 1000 times greater than the basal, uninduced level. Upon removal of the signal, that is, the inducer,
the synthesis of these three enzymes declines.

When E. coli is exposed to both lactose and glucose as sources of carbon, the cells first metabolize the glucose and then temporarily stop growing until
the genes of the lac operon become induced to provide the ability to metabolize lactose as a usable energy source. Although lactose is present from
the beginning of the bacterial growth phase, the cell does not induce those enzymes necessary for catabolism of lactose until glucose has been
exhausted. This phenomenon was first thought to be attributable to repression of the lac operon by some catabolite of glucose; hence, it was termed
catabolite repression. It is now known that catabolite repression is in fact mediated by a catabolite activator protein (CAP) in conjunction 3′, 5′
cyclic Adenosine monophosphate (cAMP; see Figure 18–5). This protein is also referred to as the cAMP regulatory protein (CRP). The expression of
many inducible enzyme systems or operons in E. coli and other prokaryotes is sensitive to catabolite repression, as discussed in following discussion.

The physiology of induction of the lac operon is well understood at the molecular level (Figure 38–3). Expression of the normal lacI gene of the lac
operon is constitutive; it is expressed at a constant rate, resulting in formation of the subunits of the lac repressor. Four identical subunits with
molecular weights of 38,000 assemble into a tetrameric Lac repressor molecule. The LacI repressor protein molecule, the product of lacI, has a very
high affinity (dissociation constant, Kd about 10−13 mol/L) for the operator locus. The operator locus is a region of double­stranded DNA that exhibits
a twofold rotational symmetry and an inverted palindrome (indicated by arrows about the dotted axis) in a region that is 21­bp long, shown as follows:

FIGURE 38–3

The mechanism of repression, derepression, and activation of the lac operon. When no inducer is present (A), the constitutively
synthesized lacI gene products form a repressor tetramer that binds to the operator. Repressor­operator binding prevents the binding of RNA
polymerase and consequently prevents transcription of the lacZ, lacY, and lacA genes into a polycistronic mRNA. When inducer is present, but glucose
is also present in the culture medium (B), the tetrameric repressor molecules are conformationally altered by inducer, and cannot efficiently bind to
the operator locus (affinity of binding reduced >1000­fold). However, RNA polymerase will not efficiently bind the promoter and initiate transcription
because positive protein–protein interactions between CRE­bound CAP protein and RNA polymerase fail to occur; thus, the lac operon is not efficiently
transcribed. However, when inducer is present, and glucose is depleted from the medium (C), adenylyl cyclase is activated and cAMP is produced. This
cAMP binds with high affinity to its binding protein the cyclic AMP activator protein, or CAP. The CAP­cAMP complex binds to its recognition sequence
(CRE, the cAMP response element) at lac operon nucleotide coordinate −50. Direct protein–protein contacts between the CRE­bound CAP and the RNA
polymerase increases promoter binding more than 20­fold; hence RNAP will efficiently transcribe the lac operon and the polycistronic lacZ­lacY­lacA
mRNA molecule formed can be translated into the corresponding protein molecules β­galactosidase, permease, and transacetylase as shown. This
protein production enables cellular catabolism of lactose as the sole carbon source for growth.

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186

Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 5 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
(CRE, the cAMP response element) at lac operon nucleotide coordinate −50. Direct protein–protein contacts between the CRE­bound CAP and the RNA
Rajiv Gandhi University of Health Sciences
polymerase increases promoter binding more than 20­fold; hence RNAP will efficiently transcribe the lac operon and the polycistronic lacZ­lacY­lacA
Access Provided by:
mRNA molecule formed can be translated into the corresponding protein molecules β­galactosidase, permease, and transacetylase as shown. This
protein production enables cellular catabolism of lactose as the sole carbon source for growth.

At any one time, only two of the four subunits of the repressor appear to bind to the operator; within the 21­base­pair operator region nearly every
base of each base pair is involved in LacI recognition and binding. Binding occurs mostly in the major groove without interrupting the base­paired,
double­helical nature of the operator DNA. The operator locus (ie, LacI binding site) is between the promoter, the site where the DNA­dependent
RNA polymerase attaches to commence transcription, and the transcription initiation site of the lacZ gene, the structural gene for β­galactosidase
(see Figures 38–2 and 36–3). When bound to the operator locus, the LacI repressor molecule prevents transcription of the distal structural genes, lacZ,
lacY, and lacA by interfering with the binding of RNA polymerase to the promoter; RNA polymerase and LacI repressor cannot be effectively bound to
the lac operon at the same time. Thus, the LacI repressor molecule is a negative regulator, and in its presence (and in the absence of inducer; see
following discussion), expression from the lacZ, lacY, and lacA genes is very, very low. There are normally about 30 repressor tetramer molecules in the
cell, a concentration (3 × 10−8 mol/L) of tetramer sufficient to effect, at any given time, more than 95% occupancy of the one lac operator element in a
bacterium, thus ensuring low (but not zero) basal lac operon gene transcription in the absence of inducing signals.

A lactose analog that is capable of inducing the lac operon while not itself serving as a substrate for β­galactosidase is an example of a gratuitous
inducer. An example is isopropylthiogalactoside (IPTG). The addition of lactose or of a gratuitous inducer such as IPTG to bacteria growing on a
poorly utilized carbon source (such as succinate) results in prompt induction of the lac operon enzymes. Small amounts of the gratuitous inducer or of
lactose are able to enter the cell even in the absence of permease. The LacI repressor molecules—both those attached to the operator loci and those
free in the cytosol—have a high affinity for the inducer. Binding of the inducer to repressor molecule induces a conformational change in the structure
of the repressor that causes a decrease in operator DNA occupancy because its affinity for the operator is now 104 times lower (Kd about 10−9 mol/L)
than that of LacI in the absence of IPTG. DNA­dependent RNA polymerase can now more efficiently compete with LacI and bind to the promoter (ie,
Figures 36–3 and 36–8), and transcription will begin, although this process is relatively inefficient (see following discussion). In such a manner, a n
inducer derepresses the lac operon and allows transcription of the genes encoding β­galactosidase, galactoside permease, and thiogalactoside
transacetylase. Translation of the polycistronic mRNA can occur even before transcription is completed. Derepression of the lac operon allows the cell
to synthesize the enzymes necessary to catabolize lactose as an energy source. Based on the physiology just described, IPTG­induced expression of
transfected plasmids bearing the lac operator–promoter ligated to appropriate bioengineered constructs is commonly used to express mammalian
recombinant proteins
Downloaded 2025­5­17 in E. coli.P Your IP is 13.233.228.186
3:44
Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 6 / 33
In orderMcGraw
©2025 for the RNA
Hill.polymerase to form a PICTerms
All Rights Reserved. at theofpromoter site most
Use • Privacy efficiently,
Policy • Noticethe cAMP­CAP complex must also be present in the cell. By an
• Accessibility
independent mechanism, the bacterium accumulates cAMP only when it is starved for a source of carbon. In the presence of glucose—or of glycerol in
concentrations sufficient for growth—the bacteria will lack sufficient cAMP to bind to CAP because glucose inhibits adenylyl cyclase, the enzyme that
Figures 36–3 and 36–8), and transcription will begin, although this process is relatively inefficient (see following discussion). In such a manner, a n
inducer derepresses the lac operon and allows transcription of the genes encoding β­galactosidase, galactoside Rajiv Gandhi University
permease, andofthiogalactoside
Health Sciences
Access Provided by:
transacetylase. Translation of the polycistronic mRNA can occur even before transcription is completed. Derepression of the lac operon allows the cell
to synthesize the enzymes necessary to catabolize lactose as an energy source. Based on the physiology just described, IPTG­induced expression of
transfected plasmids bearing the lac operator–promoter ligated to appropriate bioengineered constructs is commonly used to express mammalian
recombinant proteins in E. coli.

In order for the RNA polymerase to form a PIC at the promoter site most efficiently, the cAMP­CAP complex must also be present in the cell. By an
independent mechanism, the bacterium accumulates cAMP only when it is starved for a source of carbon. In the presence of glucose—or of glycerol in
concentrations sufficient for growth—the bacteria will lack sufficient cAMP to bind to CAP because glucose inhibits adenylyl cyclase, the enzyme that
converts ATP to cAMP (see Chapter 42). Thus, in the presence of glucose or glycerol, cAMP­saturated CAP is lacking, so that the DNA­dependent RNA
polymerase cannot initiate transcription of the lac operon at the maximal rate. However, in the presence of the CAP­cAMP complex, which binds to CAP
Response Element (CRE) DNA just upstream of the promoter site, transcription occurs at maximal levels (see Figure 38–3). Studies indicate that a
region of CAP directly contacts the RNA polymerase (RNAP) α subunit, and these protein–protein interactions facilitate the binding of RNAP to the
promoter. Thus, the CAP­cAMP regulator is acting as a positive regulator because its presence is required for optimal gene expression. The lac
operon is therefore controlled by two distinct, ligand­modulated DNA­binding trans­factors; one that acts positively (cAMP­CRP complex) to facilitate
productive binding of RNA polymerase to the promoter and one that acts negatively (LacI repressor) that antagonizes RNA polymerase promoter
binding. Maximal activity of the lac operon occurs when glucose levels are low (high cAMP with CAP activation) and lactose is present (LacI is prevented
from binding to the operator) as shown in Figure 38–3, panel C.

With the above information in hand, it becomes relatively to predict the effects of mutations in various components of the lac­system upon lac operon
expression. When the lacI gene has been mutated so that its product, LacI, is not capable of binding to operator DNA, the organism will exhibit
constitutive expression of the lac operon. In a contrary manner, an organism with a lacI gene mutation that produces a LacI protein which prevents
the binding of lactose or other small molecule inducer to the repressor will remain repressed even in the presence of the inducer molecule, because
such ligands cannot bind to the repressor on the operator locus in order to derepress the operon. Similarly, bacteria harboring mutations in their lac
operator locus such that the operator sequence will not bind a normal repressor molecule will constitutively express the lac operon genes.
Mechanisms of positive and negative regulation comparable to those described here for the lac system have been observed in eukaryotic cells (see
following discussion).

The Genetic Switch of Bacteriophage Lambda (λ) Provides Another Paradigm for Understanding the Role of
Conditional Regulatory Protein­DNA Interactions in Transcriptional Control in Eukaryotic Cells

Like some eukaryotic viruses (eg, herpes simplex virus and HIV), certain bacterial viruses can either reside in a dormant state within the host
chromosomes or can replicate within the bacterium and eventually lead to lysis and killing of the bacterial host. Some E. coli harbor such a
“temperate” virus, bacteriophage lambda (λ). When lambda infects an organism of that species, it injects its 48,490­bp, double­stranded, linear DNA
genome into the cell (Figure 38–4). Depending on the nutritional state of the cell, the lambda DNA will either integrate into the host genome
(lysogenic pathway) and remain dormant until activated (see following discussion), or it will commence replicating until it has made about 100
copies of complete, protein­packaged virus, at which point it causes lysis of its host (lytic pathway). The newly generated virus particles can then
infect other susceptible host cells. Poor growth conditions favor lysogeny while good growth conditions promote the lytic pathway of lambda growth.

FIGURE 38–4

Alternate lytic and lysogenic lifestyles of bacteriophage lambda. Infection of the bacterium E. coli by phage lambda begins when a virus
particle attaches itself to specific receptors on the bacterial cell surface (1) and injects its DNA (dark green line) into the cell (2), where the phage
genome then circularizes (3). Infection can take either of two courses depending on which two sets of viral genes is turned on. In the lysogenic
pathway, the viral DNA becomes integrated into the bacterial chromosome (r e d) (4, 5), where it is replicated passively as part of the bacterial DNA
during E. coli cell division. This dormant, bacterial genome­integrated virus is called a prophage, and the cell that harbors is called a lysogen. In the
alternative, lytic mode of infection, the viral DNA excises from the E. coli chromosome and replicates itself (6) in order to direct the synthesis of viral
proteins; black lines (7). About 100 new virus particles (green hexagons) are formed. The proliferating viruses induce lysis of the cell (8). A prophage
can be “induced” by a DNA damaging agent such as ultraviolet radiation (9). The inducing agent throws a switch (see text and Figure 38–5; the λ
“molecular switch.”), so that a different set of viral genes is turned on. Viral DNA loops out and is excised from the E. coli chromosome (1 0) and
replicates; the virus then proceeds along the lytic pathway.

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186

Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 7 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
proteins; black lines (7). About 100 new virus particles (green hexagons) are formed. The proliferating viruses induce lysis of the cell (8). A prophage
Rajiv Gandhi University of Health Sciences
can be “induced” by a DNA damaging agent such as ultraviolet radiation (9). The inducing agent throws a switch (see text and Figure 38–5; the λ
Access Provided by:
“molecular switch.”), so that a different set of viral genes is turned on. Viral DNA loops out and is excised from the E. coli chromosome (1 0) and
replicates; the virus then proceeds along the lytic pathway.

When integrated into the host genome in its dormant state, lambda will remain in that state until activated by exposure of its bacterial host to DNA­
damaging agents. In response to such a noxious stimulus, the dormant bacteriophage becomes “induced” and begins to transcribe and subsequently
translate those genes of its own genome that are necessary for its excision from the host chromosome, its DNA replication, and the synthesis of its
protein coat and lysis enzymes. This event acts like a trigger or type C (see Figure 38–1) response; that is, once dormant lambda has committed itself to
induction, there is no turning back until the cell is lysed and the replicated bacteriophage released. This switch from a dormant or prophage state to
a lytic infection is well understood at the genetic and molecular levels and will be described in detail here; though less well understood at the
molecular level, HIV and herpes viruses can behave similarly, transitioning from dormant to active states in infected humans.

The lytic/lysogenic genetic switching event in lambda is centered around an 80­bp region in its double­stranded DNA genome referred to as the “right
operator” (OR) (Figure 38–5A). The right operator is flanked on its left side by the gene for the lambda repressor protein, cI, and on its right side by
the gene encoding another regulatory protein, the c r o gene. When lambda is in its prophage state—that is, integrated into the host genome—the cI
repressor gene is the only lambda gene that is expressed. When the bacteriophage is undergoing lytic growth, the cI repressor gene is not expressed,
but the cro gene—as well as many other lambda genes—is expressed. Thus, when the cI repressor gene is on, the cro gene is off, and when the cro gene
is on, the cI repressor gene is off. As we shall see, these two genes regulate each other’s expression and thus, ultimately, the decision between lytic and
lysogenic growth of lambda. This decision between repressor gene transcription and cro gene transcription is a paradigmatic example of a molecular
transcriptional switch.

FIGURE 38–5

Downloaded 2025­5­17of
Genetic organization 3:44
thePlambda
Your IP lifestyle
is 13.233.228.186
“molecular switch.” Right operator (OR) is shown in increasing detail in this series of drawings.
Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 8 / 33
The operator
©2025 McGrawis aHill.
regionAll of the viral
Rights DNA some
Reserved. 80­bpoflong
Terms Use(A). To its left
• Privacy lies •the
Policy gene•encoding
Notice lambda repressor (cI), to its right the gene (cro)
Accessibility
encoding the regulator protein Cro. When the operator region is enlarged (B), it is seen to include three subregions termed operators: OR1, OR2, and
O 3, each 17­bp long. These three DNA elements are recognition sites to which both λ cI repressor and Cro proteins can bind. The recognition sites
is on, the cI repressor gene is off. As we shall see, these two genes regulate each other’s expression and thus, ultimately, the decision between lytic and
lysogenic growth of lambda. This decision between repressor gene transcription and cro gene transcriptionRajiv Gandhi University
is a paradigmatic of Health
example Sciences
of a molecular
transcriptional switch. Access Provided by:

FIGURE 38–5

Genetic organization of the lambda lifestyle “molecular switch.” Right operator (OR) is shown in increasing detail in this series of drawings.
The operator is a region of the viral DNA some 80­bp long (A). To its left lies the gene encoding lambda repressor (cI), to its right the gene (cro)
encoding the regulator protein Cro. When the operator region is enlarged (B), it is seen to include three subregions termed operators: OR1, OR2, and
OR3, each 17­bp long. These three DNA elements are recognition sites to which both λ cI repressor and Cro proteins can bind. The recognition sites
overlap two divergent promoters—sequences of bases to which RNA polymerase binds in order to transcribe these genes into mRNA (wavy lines) that
are translated into protein. Site OR1 is enlarged (C) to show its base sequence. (Reproduced with permission from Alan D. Iselin, artist.)

The 80­bp lambda right operator, OR, can be subdivided into three discrete, evenly spaced, 17­bp cis­active DNA elements that represent the binding
sites for either of two bacteriophage lambda regulatory proteins. Importantly, the nucleotide sequences of these three tandemly arranged sites are
similar but not identical (Figure 38–5B). The three related cis­elements, termed operators OR1, OR2, and OR3, can be bound by either cI or cro
proteins. However, the relative affinities of cI and cro for each of the sites vary, and this differential binding affinity is central to the appropriate
operation of the lambda phage lytic or lysogenic “molecular switch.” The DNA region between the cro and repressor genes also contains two promoter
sequences that direct the binding of RNA polymerase in a specified orientation, where it commences transcribing adjacent genes. One promoter
directs RNA polymerase to transcribe in the rightward direction and, thus, to transcribe cro and other distal genes, while the other promoter directs the
transcription of the cI repressor gene in the leftward direction (see Figure 38–5B).

The product of the cI repressor gene, the 236­amino­acid λ cI repressor protein is a two­domain molecule with amino terminal DNA­binding
domain (DBD) and carboxyl­terminal dimerization domain. Association of one repressor protein with another forms a dimer. cI repressor
dimers bind to operator DNA much more tightly than do monomers (Figure 38–6A, 38–6B, 38–6C).

FIGURE 38–6

Schematic molecular structures of lambda regulatory proteins cI and Cro. (A)The lambda repressor protein is a 236­amino­acid
polypeptide. The chain folds itself into a dumbbell shape with two substructures: an amino terminal (NH2) domain and a carboxyl­terminal (COOH)
domain. The two domains are linked by a region of the chain that is less structured and susceptible to cleavage by proteases (indicated by the two
arrows. (B) Single repressor molecules (monomers) tend to reversibly associate to form dimers. A dimer is held together mainly by contact between
the carboxyl­terminal domains (green hatching). (C) cI repressor dimers bind to (and can dissociate from) the recognition sites in the operator region;
they display differential affinities for the three operator sites, OR1 > OR2 > OR3. The DNA­binding domains (DBD) of the repressor molecule that makes
contact with DNA (blue hatching). (D) Cro is a single globular protein that contains both a DNA binding domain (blue hatching) and a cro­cro
dimerization domain, which promotes binding of cro­cro dimers to target operator DNA. It is important that cro exhibits the highest affinity for OR3,
opposite the sequence binding preference of the cI protein. (Reproduced with permission from Alan D. Iselin, artist.)

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186

Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 9 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
The product of the cro gene, the 66­amino­acid, 9­kDa cro protein, has a single domain but also binds the operator DNA more tightly as a dimer
(Figure 38–6D). The cro protein’s single domain mediates both operator binding and dimerization.
they display differential affinities for the three operator sites, OR1 > OR2 > OR3. The DNA­binding domains (DBD) of the repressor molecule that makes
Rajiv Gandhi University of Health Sciences
contact with DNA (blue hatching). (D) Cro is a single globular protein that contains both a DNA binding domain (blue hatching) and a cro­cro
Access Provided by:
dimerization domain, which promotes binding of cro­cro dimers to target operator DNA. It is important that cro exhibits the highest affinity for OR3,
opposite the sequence binding preference of the cI protein. (Reproduced with permission from Alan D. Iselin, artist.)

The product of the cro gene, the 66­amino­acid, 9­kDa cro protein, has a single domain but also binds the operator DNA more tightly as a dimer
(Figure 38–6D). The cro protein’s single domain mediates both operator binding and dimerization.

In a lysogenic bacterium—that is, a bacterium containing an integrated, dormant lambda prophage—the lambda repressor dimer binds preferentially
to OR1 but in so doing, by a cooperative interaction, enhances the binding (by a factor of 10) of another repressor dimer to OR2 (Figure 38–7). The
affinity of repressor for OR3 is the least of the three operator subregions. The binding of repressor to OR1 has two major effects. First, occupancy of
OR1 by repressor blocks the binding of RNA polymerase to the rightward promoter and in that way prevents expression of cro. Second, as mentioned
earlier, repressor dimer bound to OR1 enhances the binding of repressor dimer to OR2. The binding of repressor to OR2 has the important added effect
of enhancing the binding of RNA polymerase to the leftward promoter that overlaps OR3 and thereby enhances transcription and subsequent
expression of the repressor gene. This enhancement of transcription is mediated through direct protein–protein interactions between promoter­
bound RNA polymerase and OR2­bound repressor, much as described earlier for CAP protein and RNA polymerase on the lac operon. Thus, the λ cI
protein is both a negative regulator, by preventing transcription of cro, and a positive regulator, by enhancing transcription of its own gene, cI. This
dual effect of repressor is responsible for the stable state of the dormant lambda bacteriophage; not only does the repressor prevent expression of the
genes necessary for lysis, but it also promotes expression of itself to stabilize this state of differentiation. In the event that intracellular repressor
protein concentration becomes very high, the excess repressor will bind to OR3 and by so doing diminish transcription of the repressor gene from the
leftward promoter, by blocking RNAP binding to the cI promoter, until the repressor concentration drops and repressor dissociates from OR3. Similar
examples of repressor proteins also having the ability to activate transcription have been observed in eukaryotes.

FIGURE 38–7

Configuration of the lytic/lysogenic switch is shown at four stages of the lambda phage “life” cycle. The lysogenic pathway (in which the
virus remains dormant as a prophage) is selected when a repressor dimer binds to OR1, thereby making it likely that OR2 will be bound immediately by
another dimer due to the cooperative nature of cI­OR DNA binding. In the prophage (top), the repressor dimers bound at OR1 and OR2 prevent RNA
polymerase from binding to the rightward cro promoter and so block the synthesis of cro (negative control). Simultaneously these DNA­bound cI
proteins enhance the binding of polymerase to the leftward promoter (positive control), with the result that the repressor gene is transcribed into RNA
(initiation at cI gene transcription start site; TSS) and more repressor is synthesized, maintaining the lysogenic state. The prophage is induced
(middle) when ultraviolet radiation activates the protease recA, which cleaves cI repressor monomers. Induction (1) The equilibrium of free
monomers, free cI dimers, and bound dimers is thereby shifted by mass action, and cI dimers thus dissociate from the operator sites. RNA polymerase
is no longer stimulated to bind to the leftward promoter, so that repressor is no longer synthesized. As induction proceeds, Induction (2) all the
operator sites become vacant, thus polymerase can bind to the rightward promoter and cro is synthesized (cro TSS shown). During early lytic growth, a
single cro dimer binds to OR3 (light blue shaded circles), the site for which it has the highest affinity thereby occluding the cI promoter. Consequently,
RNA polymerase cannot bind to the leftward promoter, but the rightward promoter remains accessible. Polymerase continues to bind there,
transcribing cro and other early lytic genes. Lytic growth ensues (bottom). (Reproduced with permission from Alan D. Iselin, artist.)

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186

Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 10 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
operator sites become vacant, thus polymerase can bind to the rightward promoter and cro is synthesized (cro TSS shown). During early lytic growth, a
Rajiv Gandhi University of Health Sciences
single cro dimer binds to OR3 (light blue shaded circles), the site for which it has the highest affinity thereby occluding the cI promoter. Consequently,
Access Provided by:
RNA polymerase cannot bind to the leftward promoter, but the rightward promoter remains accessible. Polymerase continues to bind there,
transcribing cro and other early lytic genes. Lytic growth ensues (bottom). (Reproduced with permission from Alan D. Iselin, artist.)

With such a stable, repressive, cI­mediated, lysogenic state, one might wonder how the lytic cycle could ever be entered. However, this process does
occur quite efficiently. When a DNA­damaging signal, such as ultraviolet light, strikes the lysogenic host bacterium, fragments of single­stranded DNA
are generated that activate a specific co­protease coded by a bacterial gene and referred to as recA (see Figure 38–7). The activated recA protease
hydrolyzes the portion of the repressor protein that connects the amino­terminal and carboxyl­terminal domains of that molecule (see Figure 38–6A).
Such cleavage of the repressor domains causes the repressor dimers to dissociate, which in turn causes dissociation of the repressor molecules from
OR2 and eventually from OR1. The effects of removal of repressor from OR1 and OR2 are predictable. RNA polymerase immediately has access to the
rightward promoter and commences transcribing the cro gene, while simultaneously the enhancing effect of the repressor at OR2 on leftward
transcription is lost as well (see Figure 38–7).

The resulting newly synthesized cro protein also binds to the operator region as a dimer, but as noted earlier, its order of preference is opposite to that
of repressor (see Figure 38–7). That is, cro binds most tightly to OR3, but there is no cooperative effect of cro at OR3 on the binding of cro to OR2. At
increasingly higher concentrations of cro, the protein will bind to OR2 and eventually to OR1.

Importantly, occupancy of OR3 by cro immediately turns off transcription from the leftward cI promoter and in that way prevents any further
expression of the cI repressor gene. The molecular switch is thus completely “thrown” in the lytic direction. The cro gene is now expressed, and the
Downloaded
repressor gene2025­5­17 3:44 off.
is fully turned P Your IP is 13.233.228.186
This event is irreversible, and the expression of other lambda genes begins as part of the lytic cycle. When cro
Chapter
repressor concentration becomes quite high, itP.will
38: Regulation of Gene Expression, Anthony Weiloccupy O 1 and in so doing reduce the expression of its own gene, a process
eventually
Page 11 / 33
that is
R
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
necessary in order to drive transcription of the genes needed for the final stages of the lytic cycle.
The resulting newly synthesized cro protein also binds to the operator region as a dimer, but as noted earlier, its order of preference is opposite to that
of repressor (see Figure 38–7). That is, cro binds most tightly to OR3, but there is no cooperative effect of croRajiv
at ORGandhi
3 on theUniversity
binding ofofcro to ORSciences
Health 2. At
increasingly higher concentrations of cro, the protein will bind to OR2 and eventually to OR1. Access Provided by:

Importantly, occupancy of OR3 by cro immediately turns off transcription from the leftward cI promoter and in that way prevents any further
expression of the cI repressor gene. The molecular switch is thus completely “thrown” in the lytic direction. The cro gene is now expressed, and the
repressor gene is fully turned off. This event is irreversible, and the expression of other lambda genes begins as part of the lytic cycle. When cro
repressor concentration becomes quite high, it will eventually occupy OR1 and in so doing reduce the expression of its own gene, a process that is
necessary in order to drive transcription of the genes needed for the final stages of the lytic cycle.

The three­dimensional structures of cro and of the λ cI repressor protein have been determined by x­ray crystallography, and models for their binding
and driving the above­described molecular and genetic events have been formulated and tested. Both bind DNA using helix­turn­helix DBD motifs (see
following discussion). Along with regulation of the expression of the lac operon, the λ molecular switch described here provides arguably the best
understanding of the molecular events involved in gene transcription activation and repression.

Detailed analysis of the λ repressor led to the important concept that transcription regulatory proteins have several functional domains. For example,
lambda repressor binds to DNA with high affinity. Repressor monomers form dimers that cooperatively interact with each other, these proteins can
interact with RNA polymerase, to enhance or block promoter binding or RNAP open complex formation (see Figure 36–3). The protein­DNA interface
and the three protein–protein interfaces all involve separate and distinct domains of the two molecules. As will be noted later (see Figure 38–19), this is
a characteristic that is typical of most molecules that regulate transcription.

SPECIAL FEATURES ARE INVOLVED IN REGULATION OF EUKARYOTIC GENE TRANSCRIPTION

Most of the DNA in prokaryotic cells is organized into genes, and since the DNA is not compacted with nucleosomal histones bacterial genomes have
the potential to be transcribed if appropriate positive and negative trans­factors are present in a given cell in an active form. A very different situation
exists in eukaryotic cells for two major reasons: first, in human cells relatively little of the total DNA is organized into mRNA­encoding genes and their
associated regulatory regions. The function of the extra DNA is being actively investigated (ie, Chapter 39; the ENCODE Projects). Secondly, as described
in Chapter 35, the DNA in eukaryotic cells is extensively folded and packed into the protein­DNA complex called chromatin. Histones are an important
part of this complex since they both form the structures known as nucleosomes (see Chapter 35) and also factor significantly into gene regulatory
mechanisms as outlined in following discussion.

The Chromatin Template Contributes Importantly to Eukaryotic Gene Transcription Control

Chromatin structure provides an additional level of control of gene transcription. As discussed in Chapter 35, large regions of chromatin are
transcriptionally inactive while others are either active or potentially active. With few exceptions, each cell contains the same complement of genes;
hence, the development of specialized organs, tissues, and cells, and their function in the intact organism depend on the differential expression of
genes.

Some of this differential expression is achieved by having different regions of chromatin available for transcription in cells from various tissues. For
example, the DNA containing the β­globin gene cluster is in “active” chromatin in the reticulocyte but in “inactive” chromatin in muscle cells. All
the factors involved in the determination of active chromatin have not been elucidated. The presence of nucleosomes and of complexes of histones
and DNA (see Chapter 35) certainly provides a barrier against the ready association of most transcription factors with specific DNA regions. The
dynamics of the formation and disruption of nucleosome structure are therefore an important part of eukaryotic gene regulation.

Histone covalent modification, also dubbed the histone code, is an important determinant of gene activity. Histones are subjected to a wide
range of specific posttranslational modifications (see Table 35–1). These modifications are dynamic and reversible. Histone acetylation and
deacetylation are best understood. The surprising discovery that histone acetylase and other enzymatic activities are associated with the coregulators
involved in regulation of gene transcription (see Chapter 42 for specific examples) has provided a new concept of gene regulation. Acetylation is known
to occur on lysine residues in the amino terminal tails of histone molecules, and has been consistently correlated with either active transcription, or
alternatively, transcriptional potential. Histone acetylation reduces the positive charge of these tails and likely contributes to a decrease in the binding
affinity of histones for the negatively charged DNA. Moreover, such covalent modification of the histones creates new binding, or docking sites for
additional proteins such as ATP­dependent chromatin remodeling complexes that contain subunits that carry structural domains that specifically bind
to histones that have been subjected to coregulator­deposited PTMs. These complexes can increase accessibility of adjacent DNA sequences by
removing or otherwise altering nucleosomal histones. Together then coregulators (chromatin modifiers and chromatin remodelers), working in
conjunction, can “open up” gene promoters and regulatory regions, facilitating binding of other trans­factors such as transcriptional activator
proteins, RNA polymerase II and the GTFs (see Figures 36–10 and 36–11). Histone deacetylation catalyzed by transcriptional corepressors would have
the opposite effect.
Downloaded Different
2025­5­17 3:44proteins
P Yourwith
IP isspecific acetylase and deacetylase activities are associated with various components of the transcription
13.233.228.186
apparatus.
Chapter 38:The proteins of
Regulation that catalyze
Gene histone P.
Expression, PTMs are sometimes
Anthony Weil referred to as “code writers” while the proteins that recognize, bind,Page
and thus
12 / 33
©2025 McGraw
interpret Hill. AllPTMs
these histone Rights
areReserved.
termed “codeTerms of Use •while
readers” Privacy
the Policy
enzymes• Notice • Accessibility
that remove histone PTMs are called “code erasers.” (The analogy to
signal transduction, with its kinases, phosphatases, and phospho­amino acid binding proteins should be apparent—see Chapter 42.) Collectively then,
histone PTMs represent a very dynamic, potentially information­rich source of regulatory information. The exact rules and mechanisms defining the
additional proteins such as ATP­dependent chromatin remodeling complexes that contain subunits that carry structural domains that specifically bind
Rajiv Gandhi
to histones that have been subjected to coregulator­deposited PTMs. These complexes can increase accessibility University
of adjacent of Healthby
DNA sequences Sciences
Access Provided by:
removing or otherwise altering nucleosomal histones. Together then coregulators (chromatin modifiers and chromatin remodelers), working in
conjunction, can “open up” gene promoters and regulatory regions, facilitating binding of other trans­factors such as transcriptional activator
proteins, RNA polymerase II and the GTFs (see Figures 36–10 and 36–11). Histone deacetylation catalyzed by transcriptional corepressors would have
the opposite effect. Different proteins with specific acetylase and deacetylase activities are associated with various components of the transcription
apparatus. The proteins that catalyze histone PTMs are sometimes referred to as “code writers” while the proteins that recognize, bind, and thus
interpret these histone PTMs are termed “code readers” while the enzymes that remove histone PTMs are called “code erasers.” (The analogy to
signal transduction, with its kinases, phosphatases, and phospho­amino acid binding proteins should be apparent—see Chapter 42.) Collectively then,
histone PTMs represent a very dynamic, potentially information­rich source of regulatory information. The exact rules and mechanisms defining the
specificity of these various processes are under investigation. Some specific examples are illustrated in Chapter 42. A variety of commercial enterprises
are working to develop drugs that specifically alter the activity of the proteins that orchestrate the presence and composition of the histone code,
whose relevant PTMs continue to grow at a rapid pace (compare Table 38–2 with Table 35–1).

TABLE 38–2
Summary of Novel Histone PTMs (2011 to 2020)

Physiological
Histone PTM Reaction Donor Precursor Writer Eraser Function
Relevance

Glutarylation Acylation Glutarate Kat2a, Sirt7 Nucleosome destabilization, Glutaric acidemia

intramolecular permissive transcription
catalysis

Lactylation Acylation Lactate p300 Permissive transcription Macrophage response,

hypoxia

Benzoylation Acylation Benzoate Sirt2 Permissive transcription Sodium benzoate

treatment

S­palmitoylation S­acylation Palmitic acid Cell signaling

O­palmitoylation O­acylation Palmitic acid Lpcat1 Reduced transcription Cell signaling

Serotonylation Transamidation Serotonin Tgm2 Permissive transcription Neuronal

differentiation

Dopaminylation Transmidation Dopamine Tgm2 Altered transcription Drug­seeking behaviors

5­Hydroxylysine Hydroxylation 2­Oxoglutarate Jmjd6 Testes, development

Glycation Maillard Methylglyoxal, Nonenzymatic DJ­1 Altered nucleosome Breast cancer,

monosaccharides stability hyperglycemia

4­ Ketoamide 4­Oxo­2­nonenal Nonenzymatic Sirt2 Nucleosome destabilization Lipid peroxidation

Oxononanoylation adduction

Acrolein adduct Michael Acrolein Nonenzymatic Nucleosome destabilization Cigarette smoke, lipid
addition peroxidation

S­glutathionylation Disulfide Glutathione Nonenzymatic Nucleosome destabilization Aging

formation

Homocysteinylation Thiolation Homocysteine Nonenzymatic Reduced transcription Hyperhomocysteinemia

thyolactone

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186

Chapter 38:
Modified Regulation
with permissionoffrom
Gene Expression,
Chan P. Anthony
JC, Maze I. Nothing Weil
Is Yet Set Page 13 / 33
in (Hi)stone: Novel Post­Translational Modifications Regulating Chromatin Function, Trends
©2025 McGraw
Biochem Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
Sci. 2020;45(10):829­844.

In addition to the histone code and its effects on all DNA­mediated reactions, the methylation of deoxycytidine residues, 5meC, (in the sequence
histone PTMs represent a very dynamic, potentially information­rich source of regulatory information. The exact rules and mechanisms defining the
Rajiv Gandhi University of Health Sciences
specificity of these various processes are under investigation. Some specific examples are illustrated in Chapter 42. A variety of commercial enterprises
Access Provided by:
are working to develop drugs that specifically alter the activity of the proteins that orchestrate the presence and composition of the histone code,
whose relevant PTMs continue to grow at a rapid pace (compare Table 38–2 with Table 35–1).

TABLE 38–2
Summary of Novel Histone PTMs (2011 to 2020)

Physiological
Histone PTM Reaction Donor Precursor Writer Eraser Function
Relevance

Glutarylation Acylation Glutarate Kat2a, Sirt7 Nucleosome destabilization, Glutaric acidemia

intramolecular permissive transcription
catalysis

Lactylation Acylation Lactate p300 Permissive transcription Macrophage response,

hypoxia

Benzoylation Acylation Benzoate Sirt2 Permissive transcription Sodium benzoate

treatment

S­palmitoylation S­acylation Palmitic acid Cell signaling

O­palmitoylation O­acylation Palmitic acid Lpcat1 Reduced transcription Cell signaling

Serotonylation Transamidation Serotonin Tgm2 Permissive transcription Neuronal

differentiation

Dopaminylation Transmidation Dopamine Tgm2 Altered transcription Drug­seeking behaviors

5­Hydroxylysine Hydroxylation 2­Oxoglutarate Jmjd6 Testes, development

Glycation Maillard Methylglyoxal, Nonenzymatic DJ­1 Altered nucleosome Breast cancer,

monosaccharides stability hyperglycemia

4­ Ketoamide 4­Oxo­2­nonenal Nonenzymatic Sirt2 Nucleosome destabilization Lipid peroxidation

Oxononanoylation adduction

Acrolein adduct Michael Acrolein Nonenzymatic Nucleosome destabilization Cigarette smoke, lipid
addition peroxidation

S­glutathionylation Disulfide Glutathione Nonenzymatic Nucleosome destabilization Aging

formation

Homocysteinylation Thiolation Homocysteine Nonenzymatic Reduced transcription Hyperhomocysteinemia

thyolactone

Modified with permission from Chan JC, Maze I. Nothing Is Yet Set in (Hi)stone: Novel Post­Translational Modifications Regulating Chromatin Function, Trends
Biochem Sci. 2020;45(10):829­844.

In addition to the histone code and its effects on all DNA­mediated reactions, the methylation of deoxycytidine residues, 5meC, (in the sequence
5′­meCpG­3′) in DNA has important effects on chromatin, some of which lead to a decrease in gene transcription. For example, in mouse liver, only the
unmethylated ribosomal RNA encoding genes can be expressed, and there is evidence that many animal viruses are not transcribed when their DNA is
methylated. Acute demethylation of 5meC residues in specific regions of steroid hormone inducible genes has been associated with an increased rate
of transcription of the gene. However, as with many histone PTMs, it is not yet possible to generalize that methylated DNA is transcriptionally inactive,
Downloaded 2025­5­17
that all inactive chromatin3:44 P Your IP or
is methylated, is that
13.233.228.186
active DNA is not methylated.
Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 14 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
Finally, the binding of specific transcription factors to cognate DNA elements may result in disruption of nucleosomal structure. Most eukaryotic genes
have multiple protein­binding DNA elements. The serial binding of transcription factors to these elements—in a combinatorial fashion—may either
In addition to the histone code and its effects on all DNA­mediated reactions, the methylation of deoxycytidine residues,
Rajiv Gandhi 5meC,of
University (inHealth
the sequence
Sciences
5′­meCpG­3′) in DNA has important effects on chromatin, some of which lead to a decrease in gene transcription.
Access For example,
Provided by: in mouse liver, only the
unmethylated ribosomal RNA encoding genes can be expressed, and there is evidence that many animal viruses are not transcribed when their DNA is
methylated. Acute demethylation of 5meC residues in specific regions of steroid hormone inducible genes has been associated with an increased rate
of transcription of the gene. However, as with many histone PTMs, it is not yet possible to generalize that methylated DNA is transcriptionally inactive,
that all inactive chromatin is methylated, or that active DNA is not methylated.

Finally, the binding of specific transcription factors to cognate DNA elements may result in disruption of nucleosomal structure. Most eukaryotic genes
have multiple protein­binding DNA elements. The serial binding of transcription factors to these elements—in a combinatorial fashion—may either
directly disrupt the structure of the nucleosome, prevent its reformation, or recruit, via protein–protein interactions, multiprotein coregulator
complexes that have the ability to covalently modify and/or remodel nucleosomes. These reactions result in chromatin­level structural changes that in
the end increase or decrease DNA accessibility to other factors and the transcription machinery.

Eukaryotic DNA that is in an “active” region of chromatin can be transcribed. As in prokaryotic cells, a promoter dictates where the RNA polymerase
will initiate transcription, but the promoter in mammalian cells (see Chapter 36) is more complex. Additional complexity is added by elements or
factors that enhance or repress transcription, define tissue­specific expression, and modulate the actions of many effector molecules. Finally, recent
results suggest that gene activation and repression might occur when particular genes move into or out of different subnuclear compartments or
locations wherein variable amounts of transcription proteins and RNA either promote or disrupt biomolecular condensate formation that stimulate or
inhibit transcription.

Epigenetic Mechanisms Contribute Importantly to the Control of Gene Transcription

The molecules and regulatory biology described earlier contributes importantly to transcriptional regulation. Indeed, in recent years the role of
covalent modification of DNA and histone (and nonhistone) proteins and the newly discovered ncRNAs has received tremendous attention in the field
of gene regulation research, particularly through investigation into how such chemical modifications and/or molecules stably alter gene expression
patterns without altering the underlying DNA gene sequence. This field of study has been termed epigenetics. As mentioned in Chapter 35, one
aspect of these mechanisms, PTMs of histones has been dubbed the histone code or histone epigenetic code. The term “epigenetics” means “above
genetics” and refers to the fact that these regulatory mechanisms do not change the underlying regulated DNA sequence, but rather simply the
expression patterns, or function, of this DNA. Epigenetic mechanisms play key roles in the establishment, maintenance, and reversibility of
transcriptional states. A key feature of epigenetic mechanisms is that the controlled transcriptional on/off states can be maintained through multiple
rounds of cell division. This observation indicates that there must be robust, biochemically based mechanisms to maintain and stably propagate these
epigenetic states.

Two forms of epigenetic signals, cis­ and trans­epigenetic signals, can be described; these are schematically illustrated in Figure 38–8. A
simple trans­signaling event composed of positive transcriptional feedback mediated by an abundant, diffusible transactivator that efficiently
partitions roughly equally between mother and daughter cell at each division is depicted in Figure 38–8A. So long as the indicated, transcription factor
is expressed at a sufficient level to allow all subsequent daughter cells to inherit the trans­epigenetic signal (transcription factor), such cells will have
the cellular or molecular phenotype dictated by the other target genes of this transcriptional activator. Shown in Figure 38–8 panel B is an example of
how a cis­epigenetic signal (here as a specific meCpG methylation mark) can be stably propagated to the two daughter cells following cell division. The
hemi­methylated (ie, only one of the two DNA strands is 5meC­modified) DNA mark generated during DNA replication directs the methylation of the
newly replicated strand through the action of ubiquitous maintenance DNA methylases. Thus, the original 5meC methylation mark ultimately results in
both DNA daughter strands having the complete cis­epigenetic mark.

FIGURE 38–8

cis­ and trans­epigenetic signals. (A) An example of an epigenetic signal that acts in trans. A DNA­binding transactivator protein (yellow circle) is
transcribed from its cognate gene (yellow bar) located on a particular chromosome (blue). The expressed protein is freely diffusible between nuclear
and cytoplasmic compartments. Note that excess transactivator reenters the nucleus following cell division, binds to its own gene, and activates
transcription in both daughter cells. This cycle re­establishes the positive feedback loop that was in effect prior to cell division, and thereby enforces
stable expression of this transcriptional activator protein in both cells. (B) A cis­epigenetic signal; a gene (pink) located on a particular chromosome
(blue) carries a cis­epigenetic signal (small yellow flag) within the regulatory region upstream of the pink gene transcription unit. In this case, the
epigenetic signal is associated with active gene transcription and subsequent gene product production (pink circles). During DNA replication, the newly
replicated chromatid serves as a template that both elicits, and templates, the introduction of the same epigenetic signal, or mark, on the newly
synthesized, unmarked chromatid. Consequently, both daughter cells contain the pink gene in a similarly cis­epigenetically marked state, which
ensures expression in an identical fashion in both cells. See text for more detail.
Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186
Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 15 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
stable expression of this transcriptional activator protein in both cells. (B) A cis­epigenetic signal; a gene (pink) located on a particular chromosome
(blue) carries a cis­epigenetic signal (small yellow flag) within the regulatory region upstream of the pink gene Rajiv Gandhi University
transcription of Health
unit. In this Sciences
case, the
epigenetic signal is associated with active gene transcription and subsequent gene product production (pink circles).
Access During
Provided by: DNA replication, the newly
replicated chromatid serves as a template that both elicits, and templates, the introduction of the same epigenetic signal, or mark, on the newly
synthesized, unmarked chromatid. Consequently, both daughter cells contain the pink gene in a similarly cis­epigenetically marked state, which
ensures expression in an identical fashion in both cells. See text for more detail.

Both cis­ and trans­epigenetic signals can result in stable and hereditable expression states, and therefore generally represent type C gene expression
responses (ie, Figure 38–1). However, it is important to note that both states can be reversed if either the trans­ or cis­epigenetic signals are removed
by, for example, extinguishing the expression of the enforcing transcription factor (trans­signal) or by completely removing a DNA cis­epigenetic signal
(via DNA demethylation). Enzymes have been described that can remove both protein PTMs and 5meC modifications.

Stable transmission of epigenetic on/off states can be affected by multiple molecular mechanisms. Shown in Figure 38–9 are three ways by which cis­
epigenetic marks can be propagated through a round of DNA replication. The first example of epigenetic mark transmission involves the propagation
of DNA 5meC marks, and occurs as described in Figure 38–8. The second example of epigenetic state transmission illustrates how a nucleosomal
histone PTM (in this example, Lysine K­27 trimethylated histone H3; H3K27me3) can be propagated. In this example immediately following DNA
replication, both H3K27me3­marked and H3­unmarked nucleosomes randomly reform on both daughter DNA strands. The polycomb repressive
complex 2 (PRC2), composed of EED­SUZ12­EZH2 and RbAP subunits, binds to the nucleosome containing the preexisting H3K27me3 mark via the
EED subunit. Binding of PRC2 to this histone mark stimulates the methylase activity of the EZH2 subunit of PRC2, which results in the local methylation
of nucleosomal H3. Histone H3 methylation thus causes the full, stable transmission of the H3K27me3 epigenetic mark to both chromatids. Finally,
locus/sequence­specific targeting of nucleosomal histone epigenetic cis­signals can be attained through the action of lncRNAs as depicted in Figure
38–9, panel C. Here a specific ncRNA interacts with target DNA sequences and the resulting RNA–DNA complex is recognized by RBP, an RNA­binding
protein. Then, likely through a specific adaptor protein (A), the RNA­DNA­RBP complex recruits a chromatin modifying complex (CMC) that locally
modifies nucleosomal histones. Again, this mechanism leads to the transmission of a stable epigenetic mark.

FIGURE 38–9

Mechanisms for the transmission and propagation of epigenetic signals following a round of DNA replication. (A) Propagation of a
5meC signal (yellow flag; see Figure 38–8B). (B) Propagation of a histone PTM epigenetic signal (H3K27me) that is mediated through the action of the
PRC2, a chromatin modifying complex, or CMC. PRC2 is composed of EED, EZH2 histone methylase, RbAP, and SUZ12 subunits. Note that in this context,
PRC2 is both a histone code reader (via the methylated histone–binding domain in EED) and histone code writer (via the SET domain histone methylase
within EZH2). Location­specific deposition of the histone PTM cis­epigenetic signal is targeted by the recognition of the H3K27me marks in preexisting
nucleosomal histones (yellow flag). (C) Another example of the transmission of a histone epigenetic signal (yellow flag) except here signal­targeting is
mediated through the action of small ncRNAs that work in concert with an RNA­binding protein (RBP), an adaptor (A) protein, and a CMC. See text for
more detail. (Reproduced with permission from Bonasio R, Tu S, Reinberg D. Molecular signals of epigenetic states. Science. 2010;330(6004):612­616.)

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186

Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 16 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
within EZH2). Location­specific deposition of the histone PTM cis­epigenetic signal is targeted by the recognition of the H3K27me marks in preexisting
Rajiv Gandhi University of Health Sciences
nucleosomal histones (yellow flag). (C) Another example of the transmission of a histone epigenetic signal (yellow flag) except here signal­targeting is
Access Provided by:
mediated through the action of small ncRNAs that work in concert with an RNA­binding protein (RBP), an adaptor (A) protein, and a CMC. See text for
more detail. (Reproduced with permission from Bonasio R, Tu S, Reinberg D. Molecular signals of epigenetic states. Science. 2010;330(6004):612­616.)

Additional work will be required to establish the complete molecular details of epigenetic processes, determine how ubiquitously these mechanisms
operate, identify the full complement of molecules involved, and genes controlled. Epigenetic signals are critically important to gene regulation as
evidenced by the fact that mutations and/or overexpression of many of the molecules that contribute to epigenetic control lead to human disease.

Certain DNA Elements Enhance or Repress Transcription of Eukaryotic Genes

In addition to gross changes in chromatin affecting transcriptional activity, certain DNA elements facilitate or enhance initiation at the promoter and
hence are termed enhancers. Enhancer elements, which typically contain multiple binding sites for transactivator proteins, differ from the promoter
in notable ways. Enhancers can exert their positive influence on transcription even when separated by tens of thousands of base pairs from a
promoter; enhancers work when oriented in either direction; and enhancers can work upstream (5′) or downstream (3′) from the promoter, or even
when embedded within the transcription unit of a gene. Experimentally, enhancers can be shown to be promiscuous, in that they can stimulate
transcription of any promoter in their vicinity, and may act on more than one promoter. The viral SV40 enhancer can exert an influence on, for
example, the transcription of β­globin by increasing its transcription 200­fold in cells containing both the SV40 enhancer and the β­globin gene on the
same plasmid (see following discussion and Figure 38–10); in this case the SV40 enhancer­β­globin reporter gene was constructed using
recombinant DNA technology—see Chapter 39. The enhancer element does not produce a product that in turn acts on the promoter, since it is active
only when it exists within the same DNA molecule as the promoter (ie, in cis, or physically linked to). Enhancer­binding proteins are responsible for this
effect. The exact mechanism(s) by which these transcription activators work is subject to intensive investigation. Enhancer­binding trans­factors, some
of which are cell­type specific, while others are ubiquitously expressed, have been shown to interact with a plethora of other transcription proteins.
These interactions include chromatin­modifying coactivators, mediator, as well as the individual components of the basal RNA polymerase II
transcription machinery. Ultimately, transfactor­enhancer DNA­binding events result in an increase in the binding and/or activity of the basal
transcription machinery on the linked promoter. Enhancer elements and associated binding proteins often convey nuclease hypersensitivity to those
regions where they reside (see Chapter 35). Recently, while analyzing regulatory sequences that control cellular identity (and other genes essential for
cell function) in mammalian genomes investigators have identified large tandem clusters of various enhancer elements in tandem arrays. These
sequence elements have been termed super­enhancers. Not surprisingly, the cis­linked genes modulated by super­enhancers are highly expressed. It
is highly likely that such super­enhancers contribute importantly to the formation of the biomolecular condensates described earlier. A summary of
the properties of enhancers is presented in Table 38–2.

FIGURE 38–10

A schematic illustrating the methods used to study the organization and action of enhancers and other cis­acting regulatory
elements. These model chimeric genes, all constructed by recombinant DNA techniques in vitro (see Chapter 39), consist of a reporter gene that
Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186
encodes a protein that can be readily assayed, and that is not normally produced in the cells to be studied, a promoter that ensures accurate initiation
Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 17 / 33
of transcription,
©2025 McGraw andHill. the indicated
All Rights enhancerTerms
Reserved. (regulatory
of Useresponse)
• Privacyelements. In all cases,
Policy • Notice high­level transcription from the indicated chimeras depends
• Accessibility
on the presence of enhancers, which stimulate transcription ≥100­fold over basal transcriptional levels (ie, transcription of the same chimeric genes
containing just promoters fused to the indicated reporter genes). Examples (A) and (B) illustrate the fact that enhancers (eg, here SV40) work in either
the properties of enhancers is presented in Table 38–2.
Rajiv Gandhi University of Health Sciences
Access Provided by:
FIGURE 38–10

A schematic illustrating the methods used to study the organization and action of enhancers and other cis­acting regulatory
elements. These model chimeric genes, all constructed by recombinant DNA techniques in vitro (see Chapter 39), consist of a reporter gene that
encodes a protein that can be readily assayed, and that is not normally produced in the cells to be studied, a promoter that ensures accurate initiation
of transcription, and the indicated enhancer (regulatory response) elements. In all cases, high­level transcription from the indicated chimeras depends
on the presence of enhancers, which stimulate transcription ≥100­fold over basal transcriptional levels (ie, transcription of the same chimeric genes
containing just promoters fused to the indicated reporter genes). Examples (A) and (B) illustrate the fact that enhancers (eg, here SV40) work in either
orientation and upon a heterologous promoter. Example (C) illustrates that the metallothionein (mt) regulatory element (which under the influence of
cadmium or zinc induces transcription of the endogenous mt gene and hence the metal­binding mt protein) will work through the herpes simplex virus
(HSV) thymidine kinase (tk) gene promoter to enhance transcription of the human growth hormone (hGH) reporter gene. In a separate experiment, this
engineered genetic construct was introduced into the male pronuclei of single­cell mouse embryos and the embryos placed into the uterus of a
surrogate mother to develop as transgenic animals. Offspring have been generated under these conditions, and in some the addition of zinc ions to
their drinking water effects an increase in growth hormone expression in liver. In this case, these transgenic animals have responded to the high levels
of growth hormone by becoming twice as large as their normal litter mates. Example (D) illustrates that a glucocorticoid response element (GRE)
enhancer will work through homologous (PEPCK gene) or heterologous gene promoters (not shown; ie, HSV tk promoter, SV40 promoter, β­globin
promoter, etc) to drive expression of the chloramphenicol acetyltransferase (CAT) reporter gene.

One of the best­understood mammalian enhancer systems is that of the β­interferon gene. This gene is induced upon viral infection of mammalian
cells. One goal of the cell, once virally infected, is to attempt to mount an antiviral response—if not to save the infected cell, then to help to save the
entire organism from viral infection. Interferon production is one mechanism by which this is accomplished. This family of proteins is secreted by
virally infected cells. Secreted interferon interacts with neighboring cells to cause an inhibition of viral replication by a variety of mechanisms, thereby
limiting the extent of viral infection. The enhancer element controlling induction of the β­interferon gene, which is located between nucleotides −110
and −45 relative to the transcription start site (+1), is well characterized. This enhancer consists of four distinct clustered cis­elements, each of which is
bound by unique trans­factors. One cis­element is bound by the transacting factor NF­κB (see Figures 42–10 and 42–13), one by a member of the
interferon regulatory factor (IRF) family of transactivator factors, and a third by the heterodimeric leucine zipper factor ATF­2/c­Jun (see following
discussion). The fourth factor is the ubiquitous, abundant architectural transcription factor known as HMG I(Y). Upon binding to its A + T­rich binding
sites, HMG I(Y) induces a significant bend in the DNA. There are four such HMG I(Y) binding sites interspersed throughout the enhancer. It is believed
that these sites play a key role in facilitating the formation of a unique 3D structure in concert with the aforementioned three trans­factors, by inducing
a series of critically spaced DNA bends. Consequently, HMG I(Y) likely induces the cooperative formation of a unique, stereospecific structure within
which all four factors are active when viral infection signals are sensed by the cell. The putative structure formed by the cooperative assembly of these
four factors has been termed the β­interferon enhanceosome (Figure 38–11), so named because of its proposed structural similarity to the
nucleosome, which is also a unique three­dimensional protein­DNA structure that wraps DNA about a core assembly of proteins (see Figures 35–1 and
35–2). The enhanceosome, once formed, induces a large increase in β­interferon gene transcription upon virus infection. Thus, it is thought that it is
not simply the protein occupancy of the linearly apposed cis­element sites that induces β­interferon gene transcription—rather, it is the formation of
the enhanceosome proper that provides appropriate surfaces and 3­dimensional organization for the efficient recruitment of coactivators that results
in the enhanced formation of the PIC on the cis­linked promoter and thus transcription activation.
Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186
Chapter
FIGURE 38: Regulation of Gene Expression, P. Anthony Weil
38–11 Page 18 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
Formation and putative structure of the enhanceosome formed on the human β­interferon gene enhancer. Diagrammatically
represented at the top is the distribution of the multiple cis­elements (HMG, PRDIV, PRDI­III, PRDII, NRDI) composing the β­interferon gene enhancer.
four factors has been termed the β­interferon enhanceosome (Figure 38–11), so named because of its proposed structural similarity to the
Rajiv Gandhi
nucleosome, which is also a unique three­dimensional protein­DNA structure that wraps DNA about a core assembly University
of proteins (seeofFigures
Health35–1
Sciences
and
35–2). The enhanceosome, once formed, induces a large increase in β­interferon gene transcription upon virus
Accessinfection.
Provided by: Thus, it is thought that it is

not simply the protein occupancy of the linearly apposed cis­element sites that induces β­interferon gene transcription—rather, it is the formation of
the enhanceosome proper that provides appropriate surfaces and 3­dimensional organization for the efficient recruitment of coactivators that results
in the enhanced formation of the PIC on the cis­linked promoter and thus transcription activation.

FIGURE 38–11

Formation and putative structure of the enhanceosome formed on the human β­interferon gene enhancer. Diagrammatically
represented at the top is the distribution of the multiple cis­elements (HMG, PRDIV, PRDI­III, PRDII, NRDI) composing the β­interferon gene enhancer.
The intact enhancer mediates transcriptional induction of the β­interferon gene (IFNB1) over 100­fold upon virus infection of human cells. The cis­
elements of this modular enhancer represent the binding sites for the trans­factors HMG I(Y), cJun­ATF­2, IRF3­IRF7, and NF­κB, respectively. The
factors interact with these DNA elements in an obligatory, ordered, and highly cooperative fashion as indicated by the arrow. Initial binding of four
HMG I(Y) proteins induces sharp DNA bends in the enhancer, causing the entire 70­ to 80­bp region to assume a high level of curvature. This curvature
is integral to the subsequent highly cooperative binding of the other trans­factors since bending enables the DNA­bound factors to make critical direct
protein–protein interactions that both contribute to the formation and stability of the enhanceosome and generate a unique 3D surface that serves to
recruit chromatin­modifying coregulators that carry enzymatic activities (eg, Swi/Snf: ATPase, chromatin remodeler and P/CAF: histone
acetyltransferase) as well as the general transcription machinery (RNA polymerase II and GTFs). Although four of the five cis­elements (PRDIV, PRDI­III,
PRDII, NRDI) independently can modestly stimulate (~10­fold) transcription of a reporter gene in transfected cells (see Figures 38–10 and 38–12), all five
cis­elements, in appropriate order, are required to form an enhancer that can appropriately stimulate transcription of IFNB1 (ie, ≥100­fold) in response
to viral infection of a human cell. This distinction indicates a strict requirement for appropriate enhanceosome architecture for efficient trans­
activation. Similar enhanceosomes, involving distinct cis­ and trans­factors and coregulators, are proposed to form on many other mammalian genes.

TABLE 38–3
Summary of the Properties of Enhancers

Work when located both short and long distances from target promoter
Work when upstream or downstream from the promoter
Work when oriented in either direction
Work when embedded within target promoter
Can work with homologous or heterologous promoters
DownloadedWork by binding3:44
2025­5­17 one or
P more
Yourproteins
IP is 13.233.228.186
Chapter 38:Can
Regulation
be composed of Gene
of oneExpression, P. elements
to a few binding Anthony or
Weil
many multiples of activation elements (super enhancers) Page 19 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
Work by recruiting chromatin­modifying coregulatory complexes
Work by facilitating binding and/or function of the basal transcription complex at the cis­linked promoter
Rajiv Gandhi University of Health Sciences
Access Provided by:

TABLE 38–3
Summary of the Properties of Enhancers

Work when located both short and long distances from target promoter
Work when upstream or downstream from the promoter
Work when oriented in either direction
Work when embedded within target promoter
Can work with homologous or heterologous promoters
Work by binding one or more proteins
Can be composed of one to a few binding elements or many multiples of activation elements (super enhancers)
Work by recruiting chromatin­modifying coregulatory complexes
Work by facilitating binding and/or function of the basal transcription complex at the cis­linked promoter

cis­Acting DNA elements that decrease the expression of specific genes are termed silencers. Silencers have also been identified in a number of
eukaryotic genes. However, because fewer of these elements have been intensively studied, it is not possible to formulate accurate generalizations
about their mechanism of action. That said, it is clear that as for gene activation, chromatin level covalent modifications of histones, and other
proteins, by silencer­recruited repressors and co­recruited multisubunit corepressors likely play central roles in these regulatory events.

Tissue­Specific Expression May Result From Either the Action of Enhancers or Repressors, or a Combination of
Both cis­Acting Regulatory Elements

Most genes are now recognized to harbor enhancer elements in various locations relative to their coding regions. In addition to being able to enhance
gene transcription, some of these enhancer elements clearly possess the ability to do so in a tissue­specific manner. By fusing known or suspected
tissue­specific enhancers or silencers to reporter genes (see following discussion) and introducing these chimeric enhancer­reporter constructs via
microinjection into single­cell embryos, one can create a transgenic animal (see Chapter 39), and rigorously test whether a given test enhancer or
silencer truly modulates expression in a cell­ or tissue­specific fashion. This transgenic animal approach has proved useful in studying tissue­
specific gene expression.

Reporter Genes Are Used to Define Enhancers & Other Regulatory Elements That Modulate Gene Expression

By ligating regions of DNA suspected of harboring regulatory sequences to various reporter genes (the reporter or chimeric gene approach)
(Figures 38–10, 38–12, and 38–13), one can determine which regions in the vicinity of structural genes have an influence on their expression. Pieces
of DNA thought to harbor regulatory elements, often identified by bioinformatic sequence alignments, are ligated to a suitable reporter gene and
introduced into a host cell (see Figure 38–12). Expression of the reporter gene will be increased if the DNA contains a particular enhancer. For example,
addition of different hormones to separate cultures will increase expression of the reporter gene if the DNA contains a particular hormone response
DNA element (HRE) (see Figure 38–13; see also Chapter 42). The location of the element can be pinpointed by using progressively shorter pieces of
DNA, deletions, or and/or point mutations (see Figure 38–13).

FIGURE 38–12

The use of reporter genes to define DNA regulatory elements. A DNA fragment bearing regulatory cis­elements (triangles, square, circles in
diagram) from the gene in question—in this example, approximately 2 kb of 5′­flanking DNA and cognate promoter—is ligated into a plasmid vector
that contains a suitable reporter gene—in this case, the enzyme firefly luciferase, abbreviated LUC. As noted in Figure 38–10 in such experiments, the
reporter cannot be present endogenously in the cells transfected. Consequently, any detection of these activities in a cell extract means that the cell
was successfully transfected by the plasmid. Not shown here, but typically one cotransfects an additional reporter such as Renilla luciferase to serve as
a transfection efficiency control. Assay conditions for the firefly and Renilla luciferases are different, hence the two activities can be independently
sequentially assayed using the same cell extract. An increase of firefly luciferase activity over the basal level, for example, after addition of one or more
hormones, means that the region of DNA inserted into the reporter gene plasmid contains functional hormone response elements (HRE). Progressively
shorter pieces of DNA, regions with internal deletions, or regions with point mutations can be constructed and inserted upstream of the reporter gene
Downloaded 2025­5­17
to pinpoint the response 3:44 P Your
element IP is
(Figure 13.233.228.186
38–13). One caveat of this approach is that the transfected plasmid DNAs likely do not form “classical”
Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 20 / 33
chromatin structures.
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
reporter cannot be present endogenously in the cells transfected. Consequently, any detection of these activities in a cell extract means that the cell
Rajiv Gandhi
was successfully transfected by the plasmid. Not shown here, but typically one cotransfects an additional reporter such asUniversity of Health
Renilla luciferase toSciences
serve as
a transfection efficiency control. Assay conditions for the firefly and Renilla luciferases are different, hence the two
Access activities
Provided by: can be independently
sequentially assayed using the same cell extract. An increase of firefly luciferase activity over the basal level, for example, after addition of one or more
hormones, means that the region of DNA inserted into the reporter gene plasmid contains functional hormone response elements (HRE). Progressively
shorter pieces of DNA, regions with internal deletions, or regions with point mutations can be constructed and inserted upstream of the reporter gene
to pinpoint the response element (Figure 38–13). One caveat of this approach is that the transfected plasmid DNAs likely do not form “classical”
chromatin structures.

FIGURE 38–13

Mapping distinct hormone response elements (HREs) (A), (B), and (C) using the reporter gene–transfection approach. A family of
reporter genes, constructed as described in Figures 38–10 and 38–12, can be transfected individually into recipient cells. By analyzing when certain
hormone responses are lost in comparison to the 5′ deletion end point, specific hormone­response enhancer elements can be located and defined,
ultimately with nucleotide­level precision (see summary, bottom).

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186

Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 21 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
Mapping distinct hormone response elements (HREs) (A), (B), and (C) using the reporter gene–transfection approach. A family of
Rajiv Gandhi University of Health Sciences
reporter genes, constructed as described in Figures 38–10 and 38–12, can be transfected individually into recipient cells. By analyzing when certain
Access Provided by:
hormone responses are lost in comparison to the 5′ deletion end point, specific hormone­response enhancer elements can be located and defined,
ultimately with nucleotide­level precision (see summary, bottom).

This strategy, typically performed using transfected cells in culture (ie, cells induced to take up exogenous DNAs), has led to the identification of
hundreds of enhancers, silencers/repressors such as tissue­specific elements, and hormone, heavy metal, and drug­response elements. The activity of
a gene at any moment reflects the interaction of these numerous cis­acting DNA elements with their respective trans­acting factors. Overall,
transcriptional output is determined by the balance of positive and negative signaling to the transcription machinery. The challenge now is to figure
out exactly how this regulation occurs at the molecular level so that we might ultimately have the ability to modulate gene transcription therapeutically.

Combinations of DNA Elements & Associated Proteins Provide Diversity in Responses

Prokaryotic genes are often regulated in an on­off manner in response to simple environmental cues. Some eukaryotic genes are regulated in the
simple on­off manner, but the process in most genes, especially in mammals, is much more complicated. Signals representing a number of complex
environmental stimuli may converge on a single gene. The response of the gene to these signals can have several physiologic characteristics. First, the
response may extend over a considerable range. This is accomplished by having additive and synergistic positive responses counterbalanced by
negative or repressing effects. In some cases, either the positive or the negative response can be dominant. Also required is a mechanism whereby an
effector, such as a hormone, can activate some genes in a cell while repressing others and leaving still others unaffected. When all of these processes
are coupled with tissue­specific element factors, considerable flexibility is afforded. These physiologic variables obviously require an arrangement
much more complicated than an on­off switch. The collection and organization of DNA elements in a promoter specifies—via associated factors—how
a given gene will respond, and how long a particular response is maintained. Some simple examples are illustrated in Figure 38–14.

FIGURE 38–14

Combinations of DNA elements and proteins provide diversity in the response of a gene. Gene A is activated (the width of the arrow, right,
indicates the extent) by the combination of transcriptional activator proteins 1, 2, and 3 (with coactivators, as shown in Figures 36–10 and 38–11). Gene
B is activated, in this case more effectively, by the combination of factors 1, 3, and 4; note that transcription factor 4 does not contact DNA directly in
this example. The activators could form a linear bridge that links the basal machinery to the promoter, or alternatively, this could be accomplished by
DNA looping, or 3D structure formation (ie, Figure 38–11). Regardless, the purpose is to direct the basal transcription machinery to the promoter. Gene
C is inactivated by the combination of transcription factors 1, 5, and 3; in this case, factor 5 is shown to preclude the essential binding of factor 2 to
DNA, as occurs in example A. If activator 1 promotes cooperative binding of repressor protein 5, and if activator 1 binding requires a ligand (solid dot),
it can be seen how the ligand could activate one gene in a cell (gene A) and repress another (gene C) in the same cell.

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186

Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 22 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
DNA looping, or 3D structure formation (ie, Figure 38–11). Regardless, the purpose is to direct the basal transcription machinery to the promoter. Gene
Rajiv Gandhi University of Health Sciences
C is inactivated by the combination of transcription factors 1, 5, and 3; in this case, factor 5 is shown to preclude the essential binding of factor 2 to
Access Provided by:
DNA, as occurs in example A. If activator 1 promotes cooperative binding of repressor protein 5, and if activator 1 binding requires a ligand (solid dot),
it can be seen how the ligand could activate one gene in a cell (gene A) and repress another (gene C) in the same cell.

Transcription Domains Can Be Defined by Variable 3­D Localization Within the Cell

The large number of genes in eukaryotic cells and the complex arrays of transcription regulatory factors present an organizational problem. Why are
some genes available for transcription in a given cell whereas others are not? If enhancers can regulate several genes from tens of kilobase distances
and are not obligatorily position­ and orientation­dependent, how are they prevented from triggering transcription of all cis­linked genes in the
vicinity? Part of the solution to these problems is arrived at by having the chromatin arranged in functional units that restrict patterns of gene
expression. This may be achieved by having the chromatin form a structure with the nuclear matrix or other physical entity or compartment within the
nucleus. On a macro­scale, the 4D Nucleome Project, an international consortium of scientists studying nuclear function, aims to analyze nuclear
genome structure and dynamics to gain insights into how these features map onto transcriptional activity. On a gene­by­gene scale, a molecular
mechanism to focus enhancer­driven transcription is provided by insulators. These DNA elements, also in association with one or more specific
proteins, prevent an enhancer from acting on a promoter on the other side of an insulator in another transcription domain. Insulators thus serve as
transcriptional boundary elements. In the globin gene cluster, and many other genes, enhancer and promoter sequences are brought into physical
contact via specific DNA looping events, often involving boundary elements. The rules controlling such chromosome looping are currently under
intense study.

SEVERAL STRUCTURAL MOTIFS COMPOSE THE DNA­BINDING DOMAINS OF REGULATORY

TRANSCRIPTION FACTOR PROTEINS
The specificity involved in the control of transcription requires that regulatory proteins bind with high affinity and specificity to the correct region of
DNA. Three unique motifs—the helix­turn­helix (HTH), the zinc finger (ZF), and the leucine zipper (LZ)—account for many of these specific
protein­DNA interactions. Examples of proteins containing these motifs are given in Table 38–4.

TABLE 38–4
Examples of Transcription Factors That Contain Various DNA­Binding Motifs

Binding Motif Organism Regulatory Protein

Helix­turn­helix E. coli lac repressor, CAP

Phage λcI, cro, and 434 repressors
Mammals Homeobox proteins Pit­1, Oct1, Oct2

Zinc finger E. coli Gene 32 protein

Yeast Gal4
Drosophila Serendipity, hunchback
Xenopus TFIIIA
Downloaded 2025­5­17 3:44 PMammals
Your IP is 13.233.228.186
Steroid receptor family, Sp1
Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 23 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
Leucine zipper Yeast GCN4
Mammals C/EBP, fos, Jun, Fra­1, CRE binding protein (CREB), c­myc, n­myc, I­myc
TRANSCRIPTION FACTOR PROTEINS
Rajiv Gandhi University of Health Sciences
The specificity involved in the control of transcription requires that regulatory proteins bind with high affinity and specificity to the correct region of
Access Provided by:
DNA. Three unique motifs—the helix­turn­helix (HTH), the zinc finger (ZF), and the leucine zipper (LZ)—account for many of these specific
protein­DNA interactions. Examples of proteins containing these motifs are given in Table 38–4.

TABLE 38–4
Examples of Transcription Factors That Contain Various DNA­Binding Motifs

Binding Motif Organism Regulatory Protein

Helix­turn­helix E. coli lac repressor, CAP

Phage λcI, cro, and 434 repressors
Mammals Homeobox proteins Pit­1, Oct1, Oct2

Zinc finger E. coli Gene 32 protein

Yeast Gal4
Drosophila Serendipity, hunchback
Xenopus TFIIIA
Mammals Steroid receptor family, Sp1

Leucine zipper Yeast GCN4

Mammals C/EBP, fos, Jun, Fra­1, CRE binding protein (CREB), c­myc, n­myc, I­myc

Comparison of the binding activities of the proteins that contain these motifs leads to several important generalizations.

1. Binding must be of high affinity to the specific site, and of low affinity to all other DNA.

2. Small regions of the protein make direct contact with DNA; the rest of the protein, in addition to providing the trans­activation domains, may be
involved in the dimerization of monomers of the binding protein, may provide a contact surface for the formation of heterodimers, may provide
one or more ligand­binding sites, or may provide surfaces for interaction with coactivators, corepressors, or the transcription machinery.

3. The protein­DNA interactions made by these proteins are maintained by hydrogen bonds, ionic interactions, and van der Waals forces.

4. The motifs found in these proteins are class­specific; their presence in a protein of unknown function suggests that the protein may bind to DNA.

5. Proteins with the helix­turn­helix or leucine zipper motifs form dimers, and their respective DNA­binding sites are symmetric palindromes. In
proteins with the zinc finger motif, the binding site is repeated two to nine times. These features allow for cooperative interactions between
binding sites and enhance the degree and affinity of binding.

The Helix­Turn­Helix Motif

The first motif described was the helix­turn­helix. Analysis of the 3D structure of the lambda cro transcription regulator revealed that each monomer
consists of three antiparallel β sheets and three α helices (Figure 38–15). The dimer forms by association of the antiparallel β3 sheets. The α3 helices
form the DNA recognition surface, and the rest of the molecule appears to be involved in stabilizing these structures. The average diameter of an α
helix is 1.2 nm, which is the approximate width of the major groove in the B form of DNA.

FIGURE 38–15

A schematic representation of the 3D structure of Cro protein and its binding to DNA by its helix­turn­helix motif (left). The cro
monomer consists of three antiparallel β sheets (β1­β3) and three α helices (α1­α3). The helix­turn­helix (HTH) motif is formed because the α3 and α2
helices are held at about 90° to each other by a turn of four amino acids. The α3 helix of cro is the DNA recognition surface (shaded). Two monomers
associate through interactions between the two antiparallel β3 sheets to form a dimer that has a twofold axis of symmetry (right). A cro dimer binds to
DNA through its α3 helices, each of which contacts about 5 bp on the same face of the major groove (see Figures 34–2 and 38–6). The distance between
comparable points on the two DNA α helices is 34 Å, the distance required for one complete turn of the double helix. (Reproduced with permission
from B Mathews.)
Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186
Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 24 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
helices are held at about 90° to each other by a turn of four amino acids. The α3 helix of cro is the DNA recognition surface (shaded). Two monomers
Rajiv Gandhi University of Health Sciences
associate through interactions between the two antiparallel β3 sheets to form a dimer that has a twofold axisAccess
of symmetry
Provided by:
(right). A cro dimer binds to
DNA through its α3 helices, each of which contacts about 5 bp on the same face of the major groove (see Figures 34–2 and 38–6). The distance between
comparable points on the two DNA α helices is 34 Å, the distance required for one complete turn of the double helix. (Reproduced with permission
from B Mathews.)

The DNA recognition domain of each cro monomer interacts with 5 bp and the dimer­binding sites span 3.4 nm, allowing it to fit into successive half
turns of the major groove on the same surface of DNA (see Figure 38–15). X­ray analyses of the λ cI repressor, CAP (the cAMP receptor protein of E. coli),
tryptophan repressor, and phage 434 repressor, all also display this dimeric helix­turn­helix structure, which is also present in many eukaryotic DNA­
binding proteins (see Table 38–4).

The Zinc Finger Motif

The zinc finger was the second DNA­binding motif whose atomic structure was elucidated. It was known that the eukaryotic protein involved, a
positive regulator of 5S RNA gene transcription termed TFIIIA, required zinc for activity. Structural and biophysical analyses revealed that each TFIIIA
molecule contains nine zinc ions in a repeating coordination complex formed by closely spaced cysteine–cysteine residues followed 12 to 13 amino
acids later by a histidine–histidine pair (Figure 38–16). In some instances—notably the steroid–thyroid nuclear hormone receptor family—the His–His
doublet is replaced by a second Cys–Cys pair. The zinc finger motifs of the protein lie on one face of the DNA helix, with successive fingers alternatively
positioned in one turn in the major groove. As is the case with the recognition domain in the helix­turn­helix protein, each TFIIIA zinc finger contacts
about 5 bp of DNA. The importance of this motif in the action of steroid hormones is underscored by an “experiment of nature.” A single amino acid
mutation in either of the two zinc fingers of the 1,25(OH)2­D3 receptor protein results in resistance to the action of this hormone and the clinical
syndrome of rickets.

FIGURE 38–16

Zinc fingers are a series of repeated domains (two to nine) in which each is centered on a tetrahedral coordination with zinc. In the
case of the DNA­binding transcription factor TFIIIA, the coordination is provided by a pair of cysteine residues (C) separated by 12 to 13 amino acids
from a pair of histidine (H) residues. In other zinc finger proteins, the second pair also consists of C residues. Zinc fingers bind in the major groove,
where adjacent Zn­fingers make contact with 5 bp of DNA along the same face of the helix.

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186

Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 25 / 33
The Leucine
©2025 McGraw Zipper MotifReserved. Terms of Use • Privacy Policy • Notice • Accessibility
Hill. All Rights

Analysis of a 30­amino­acid sequence in the carboxyl­terminal region of the mammalian enhancer­binding protein C/EBP revealed a novel structure,
Zinc fingers are a series of repeated domains (two to nine) in which each is centered on a tetrahedral coordination with zinc. In the
Rajiv Gandhi University of Health Sciences
case of the DNA­binding transcription factor TFIIIA, the coordination is provided by a pair of cysteine residues (C) separated by 12 to 13 amino acids
Access Provided by:
from a pair of histidine (H) residues. In other zinc finger proteins, the second pair also consists of C residues. Zinc fingers bind in the major groove,
where adjacent Zn­fingers make contact with 5 bp of DNA along the same face of the helix.

The Leucine Zipper Motif

Analysis of a 30­amino­acid sequence in the carboxyl­terminal region of the mammalian enhancer­binding protein C/EBP revealed a novel structure,
the leucine zipper motif. As illustrated in Figure 38–17, this region of the protein forms an α helix in which there is a periodic repeat of leucine
residues at every seventh position. This occurs for eight helical turns and four leucine repeats. Similar structures have been found in a number of
other proteins associated with the regulation of transcription in all eukaryotes tested. This structure allows two identical or nonidentical monomers
(eg, Jun–Jun or Fos–Jun) to “zip together” in a coiled coil and form a tight dimeric complex (see Figure 38–17). This protein–protein interaction serves
to enhance the association of the separate DBDs with their target DNA sites (see Figure 38–17).

FIGURE 38–17

The leucine zipper motif. (A) Shown is a helical wheel analysis of a carboxyl­terminal portion of the DNA­binding protein C/EBP (see Table 36–3).
The amino acid sequence is displayed end­to­end down the axis of a schematic α helix (see Figures 5–2, 5–3, 5–4). The helical wheel consists of seven
spokes that correspond to the seven amino acids that comprise every two turns of the α helix. Note that leucine residues (L) occur at every seventh
position (in this schematic C/EBP amino acid residues 1, 8, 15, 22; see arrow). Other proteins with “leucine zippers” have a similar helical wheel pattern.
(B) A schematic model of the DNA­binding domain of C/EBP. Two identical C/EBP polypeptide chains are held in dimer formation by the leucine zipper
domain of each polypeptide (denoted by the white rectangles and attached orange­shaded ovals). This association is required to hold the DNA­binding
domains of each polypeptide (the green­shaded rectangles) in the proper conformation and register for DNA binding. (Reproduced with permission
from S McKnight.)

THE DNA BINDING & TRANSACTIVATION DOMAINS OF MOST REGULATORY PROTEINS ARE
SEPARATE
DNA binding could result in a general conformational change that allows the bound protein to activate transcription, alternatively these two functions
Downloaded 2025­5­17
could be served 3:44
by separate P independent
and Your IP is 13.233.228.186
domains. Domain swap experiments suggest that the latter is typically the case. The critical tests to
Chapter 38: Regulation of Gene Expression,
address this question was first performed P. yeast
in the Anthony Weil
Saccharomyces cerevisiae.
Page 26 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
The yeast GAL1 gene is a member of a group of genes involved in galactose metabolism. Transcription of GAL1 is controlled by the DNA­binding
transactivator protein Gal4. Gal4 binds to a 17bp enhancer element (termed upstream activator sequence, or UAS in yeast) located upstream of the
Rajiv Gandhi University of Health Sciences
THE DNA BINDING & TRANSACTIVATION DOMAINS OF MOST REGULATORY
Access Provided by:PROTEINS ARE

SEPARATE
DNA binding could result in a general conformational change that allows the bound protein to activate transcription, alternatively these two functions
could be served by separate and independent domains. Domain swap experiments suggest that the latter is typically the case. The critical tests to
address this question was first performed in the yeast Saccharomyces cerevisiae.

The yeast GAL1 gene is a member of a group of genes involved in galactose metabolism. Transcription of GAL1 is controlled by the DNA­binding
transactivator protein Gal4. Gal4 binds to a 17bp enhancer element (termed upstream activator sequence, or UAS in yeast) located upstream of the
Gal1 promoter via its N­terminal DNA binding domain (DBD; Gal4 amino acids 1­73). Gal4 activates GAL1 transcription through a C­terminal 34 aa
activation domain (AD). To systematically test the contributions of the Gal4 AD and DBD sequences to GAL1 gene transcription activation, and to ask
whether the Gal4 DBD uniquely contributed to such transcription activation, a series of domain swap experiments were performed (Figure 38–18).
The amino terminal 73­amino­acid DBD of Gal4 was removed and replaced with the DBD of LexA, an E. coli DNA­binding protein. This domain swap
resulted in a chimeric molecule (lexA DBD­Gal4 AD) that did not bind to the GAL1 UAS, and did not activate transcription of the GAL1 gene as might be
expected (see Figure 38–18). If, however, the lexA operator—the DNA sequence normally bound by the LexA DBD—was inserted upstream of the
promoter of the GAL gene to replace the normal GAL1 enhancer, the hybrid LexA­Gal4 AD fusion protein bound to this chimeric gene (at the substituted
lexA operator) and activated transcription of GAL1. This general experiment has been repeated many times with a large array of different DBDs and
ADs. Collectively, such data demonstrates that the DBDs and ADs of many transcription factors can function independently.

FIGURE 38–18

Domain­swap experiments demonstrate the independent nature of DNA­binding and transcription activation domains. The yeast
GAL1 gene contains an upstream activating sequence/enhancer (UASGAL/Enhancer) that is bound by the multi­domain DNA binding regulatory
transcriptional activator protein Gal4. Gal4, like the lambda cI protein is modular, and contains an N­terminal DNA binding domain (DBD) and a C­
terminal activation domain (AD). When the intact Gal4 transcription factor binds the GAL1 UASGAL enhancer, activation of GAL1 gene transcription
ensues [(A); Active]. Control experiments demonstrate that all three GAL1­gene specific components [ie. cis­ and trans­active components: UASGAL
DNA enhancer, Gal4 DBD and Gal4 AD) are required for active transcription of the natural GAL1 gene, as expected [(B), (C), (D), (E), (F)­all Inactive]. A
chimeric protein, in which the DBD of Gal4 is replaced with the DBD of the E coli­specific operator DNA binding protein LexA fails to stimulate GAL1
transcription because the LexA DBD cannot bind to the UASGAL/Enhancer [(G); Inactive]. By contrast, the LexA DBD­Gal4 AD fusion protein does
activate GAL1 transcription when the LexA operator (the natural target for the LexA DBD) is inserted upstream of the GAL1 promoter region, replacing
the normal UASGAL/Enhancer [(H); Active].

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186

Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 27 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
chimeric protein, in which the DBD of Gal4 is replaced with the DBD of the E coli­specific operator DNA binding protein LexA fails to stimulate GAL1
transcription because the LexA DBD cannot bind to the UASGAL/Enhancer [(G); Inactive]. By contrast, the LexA Rajiv Gandhi AD
DBD­Gal4 University of Health
fusion protein Sciences
does
Access Provided by:
activate GAL1 transcription when the LexA operator (the natural target for the LexA DBD) is inserted upstream of the GAL1 promoter region, replacing
the normal UASGAL/Enhancer [(H); Active].

The hierarchy involved in assembling gene transcription­activating complexes includes proteins that bind DNA and transactivate; others that form
protein–protein complexes which bridge DNA­binding proteins to transactivating proteins; and others that form protein–protein complexes with
components of coregulators or the basal transcription apparatus. A given protein may thus have several modular surfaces or domains that serve
different functions (Figure 38–19). As described in Chapter 36, the primary purpose of these molecules is to facilitate the assembly and/or activity of
the basal transcription apparatus on the cis­linked promoter. Not shown here, but DNA­binding repressor proteins are organized similarly with
separable DBDs and silencing domains, SDs.

FIGURE 38–19

Proteins that2025­5­17
Downloaded regulate3:44transcription have
P Your IP is several domains. This hypothetical transcription factor has a DBD that is distinct from a ligand­
13.233.228.186
Chapter 38: Regulation of Gene Expression, P. Anthony
binding domain (LBD) and several activation domains Weil
(ADs) Page
(1­4). Other proteins may lack the DBD or LBD and all may have variable numbers of28 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility
domains that contact other proteins, including coregulators and those of the basal transcription complex (see also Chapters 41 and 42).
different functions (Figure 38–19). As described in Chapter 36, the primary purpose of these molecules is to facilitate the assembly and/or activity of
the basal transcription apparatus on the cis­linked promoter. Not shown here, but DNA­binding repressor proteins are organized
Rajiv Gandhi similarly
University with
of Health Sciences
separable DBDs and silencing domains, SDs. Access Provided by:

FIGURE 38–19

Proteins that regulate transcription have several domains. This hypothetical transcription factor has a DBD that is distinct from a ligand­
binding domain (LBD) and several activation domains (ADs) (1­4). Other proteins may lack the DBD or LBD and all may have variable numbers of
domains that contact other proteins, including coregulators and those of the basal transcription complex (see also Chapters 41 and 42).

GENE REGULATION IN PROKARYOTES & EUKARYOTES DIFFERS IN OTHER IMPORTANT

RESPECTS
In addition to transcription, eukaryotic cells employ a variety of other mechanisms to regulate gene expression (Table 38–5). Many more steps,
especially in RNA processing, are involved in the expression of eukaryotic genes than of prokaryotic genes, and these steps provide additional sites for
regulatory influences that cannot exist in prokaryotes. These RNA processing steps in eukaryotes, described in detail in Chapter 36, include capping of
the 5′ ends of primary transcripts, addition of a polyadenylate tail to the 3′ ends of transcripts, mRNA internal base modifications and excision of intron
regions to generate spliced exons in the mature mRNA molecule. To date, analyses of eukaryotic gene expression provide evidence that regulation
occurs at the level of transcription, nuclear RNA processing, nuclear transport, mRNA stability, and translation. In addition, gene amplification and
rearrangement influence gene expression.

TABLE 38–5
Gene Expression Is Regulated by Transcription & in Numerous Other Ways in Eukaryotic Cells

Gene amplification
Gene rearrangement
RNA processing
Alternate mRNA splicing
Transport of mRNA from nucleus to cytoplasm
Regulation of mRNA stability
mRNA compartmentalization
Translational control
ncRNA silencing and activation

Owing to the advent of recombinant DNA technology and high throughput DNA, RNA and protein sequencing methods and other new genetic tools (see
Chapter 39), much progress has been made in recent years in our understanding of eukaryotic gene expression. However, because most eukaryotic
organisms contain so much more genetic information than do prokaryotes, and because manipulation of their genes is more difficult, molecular
aspects of eukaryotic gene regulation are less well understood than the examples discussed earlier in this chapter. This section briefly describes a few
different types of eukaryotic gene regulation.

ncRNAs Modulate Gene Expression by Altering mRNA Function

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186
As noted38:
Chapter in Chapter 35, the
Regulation recently
of Gene discovered
Expression, P.class of ubiquitous
Anthony Weil large and small eukaryotic (non–protein­coding) ncRNAs contribute importantly to
Page 29 / 33
©2025 McGraw
the control Hill.
of gene All Rights The
expression. Reserved. Terms
mechanism of Useof• the
of action Privacy
smallPolicy
miRNA • Notice • Accessibility
and siRNAs are best understood. These ~22 nucleotide RNAs regulate the
function/expression of specific mRNAs by either inhibiting translation or inducing mRNA degradation via different mechanisms; in a very few cases
miRNAs have been shown to stimulate mRNA function. miRNA action can result in dramatic changes in protein production and hence gene expression.
Chapter 39), much progress has been made in recent years in our understanding of eukaryotic gene expression. However, because most eukaryotic
Rajiv Gandhi University of Health Sciences
organisms contain so much more genetic information than do prokaryotes, and because manipulation of their genes is more difficult, molecular
Access Provided by:
aspects of eukaryotic gene regulation are less well understood than the examples discussed earlier in this chapter. This section briefly describes a few
different types of eukaryotic gene regulation.

ncRNAs Modulate Gene Expression by Altering mRNA Function

As noted in Chapter 35, the recently discovered class of ubiquitous large and small eukaryotic (non–protein­coding) ncRNAs contribute importantly to
the control of gene expression. The mechanism of action of the small miRNA and siRNAs are best understood. These ~22 nucleotide RNAs regulate the
function/expression of specific mRNAs by either inhibiting translation or inducing mRNA degradation via different mechanisms; in a very few cases
miRNAs have been shown to stimulate mRNA function. miRNA action can result in dramatic changes in protein production and hence gene expression.
These small ncRNAs have been implicated in numerous human diseases such as heart disease, cancer, muscle wasting, viral infection, and diabetes.

miRNAs and siRNAs, like the DNA­binding transcription factors described in detail earlier, are transactive, and once synthesized and appropriately
processed, interact with specific proteins and bind target mRNAs (see Figure 36–17). Binding of miRNAs to mRNA targets is directed by normal base­
pairing rules. In general, if miRNA–mRNA base pairing has one or more mismatches, translation of the cognate “target” mRNA is inhibited, whereas if
miRNA–mRNA base pairing is perfect over all 22 nucleotides, the corresponding mRNA is degraded.

Given the tremendous and ever­growing importance of miRNAs, many scientists and biotechnology companies are actively studying miRNA biogenesis,
transport, and function in hopes of curing human disease. Time will tell the magnitude and universality of ncRNA­mediated gene regulation.

Eukaryotic Genes Can Be Amplified or Rearranged During Development or in Response to Drugs

During early development of metazoans, there is an abrupt increase in the need for specific molecules such as ribosomal RNA and messenger RNA
molecules for proteins that make up specific cell or tissue types. One way to increase the rate at which such molecules can be formed is to increase the
number of genes available for transcription of these specific molecules. Among the repetitive DNA sequences within the genome are hundreds of
copies of ribosomal RNA­encoding genes. These genes preexist repetitively in the DNA of the gametes and thus are transmitted in high copy numbers
from generation to generation. In some specific organisms such as the fruit fly (Drosophila), there occurs during oogenesis an amplification of a few
preexisting genes such as those for the chorion (eggshell) proteins. Subsequently, these amplified genes, presumably generated by a process of
repeated initiations during DNA synthesis, provide multiple sites for gene transcription (see Figures 36–4 and 38–20). The dark side of specific gene
amplification is the fact that in human cancer cells drug resistance can develop upon extended therapeutic treatment due to the amplification and
increased expression of genes that encode proteins that either degrade, or pump drugs from target cells.

FIGURE 38–20

Schematic representation of the amplification of chorion protein­encoding genes s 3 6 and s 3 8. (Reproduced with permission from
Chisholm R: Gene amplification during development, Trends Biochem Sci 1982;7(5):161­162.)

As noted in Chapter 36, the coding sequences responsible for the generation of specific protein molecules are frequently not contiguous in the
mammalian genome. In the case of antibody encoding genes, this is particularly true. As described in detail in Chapter 52, immunoglobulins are
composed of two polypeptides, the so­called heavy (about 50 kDa) and light (about 25 kDa) chains. The mRNAs encoding these two protein subunits
are encoded by gene sequences that are subjected to extensive DNA sequence–coding changes. These DNA coding changes are integral to generating
the requisite recognition diversity central to appropriate immune function.

IgG heavy­ and light­chain mRNAs are encoded by several different segments that are tandemly repeated in the germline. Thus, for example, the IgG
light chain consists of variable (VL), joining (JL), and constant (CL) domains or segments. For particular subsets of IgG light chains, there are roughly 300
Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186
tandemly repeated VL gene coding segments, 5 tandemly arranged JL coding sequences, and roughly 10 CL gene coding segments. All of these Pagemultiple,
Chapter 38: Regulation of Gene Expression, P. Anthony Weil 30 / 33
©2025
distinctMcGraw Hill. All Rights
coding sequences Reserved.
are located in the Terms of Useof• the
same region Privacy
samePolicy • Notice and
chromosome, • Accessibility
each type of coding segment (VL, JL, and CL) is tandemly
repeated in head­to­tail fashion within the segment repeat region. By having multiple VL, JL, and CL segments to choose from, an immune cell has a
composed of two polypeptides, the so­called heavy (about 50 kDa) and light (about 25 kDa) chains. The mRNAs encoding these two protein subunits
Rajiv Gandhi University of Health Sciences
are encoded by gene sequences that are subjected to extensive DNA sequence–coding changes. These DNA coding changes are integral to generating
Access Provided by:
the requisite recognition diversity central to appropriate immune function.

IgG heavy­ and light­chain mRNAs are encoded by several different segments that are tandemly repeated in the germline. Thus, for example, the IgG
light chain consists of variable (VL), joining (JL), and constant (CL) domains or segments. For particular subsets of IgG light chains, there are roughly 300
tandemly repeated VL gene coding segments, 5 tandemly arranged JL coding sequences, and roughly 10 CL gene coding segments. All of these multiple,
distinct coding sequences are located in the same region of the same chromosome, and each type of coding segment (VL, JL, and CL) is tandemly
repeated in head­to­tail fashion within the segment repeat region. By having multiple VL, JL, and CL segments to choose from, an immune cell has a
greater repertoire of sequences to work with to develop both immunologic flexibility and specificity. However, a given functional IgG light­chain
transcription unit—like all other “normal” mammalian transcription units—contains only the coding sequences for a single protein. Thus, before a
particular IgG light chain can be expressed, single VL, JL, and CL coding sequences must be recombined to generate a single, contiguous transcription
unit excluding the multiple nonutilized segments (ie, the other approximately 300 unused VL segments, the other 4 unused JL segments, and the other
9 unused CL segments). This deletion of unused genetic information is accomplished by selective DNA recombination that removes the unwanted
coding DNA while retaining the required coding sequences: one VL, one JL, and one CL sequence. (VL sequences are subjected to additional point
mutagenesis to generate even more variability—hence the name.) The newly recombined sequences thus form a single transcription unit that is
competent for RNA polymerase II–mediated transcription into a single monocistronic IgG light chain­encoding mRNA. These multiple IgG­gene
recombination and mutation events are generated in a single clonal population of B­cells. Although the IgG genes represent one of the best­studied
instances of directed DNA rearrangement modulating gene expression, other cases of gene regulatory DNA rearrangement have been described.

Alternative RNA Processing Is Another Control Mechanism

In addition to affecting the efficiency of promoter utilization, eukaryotic cells employ alternative RNA processing to control gene expression. This can
result when alternative promoters, intron–exon splice sites, or polyadenylation sites are used. Occasionally, heterogeneity within a cell results, but
more commonly the same primary transcript is processed differently in different tissues. A few examples of each of these types of regulation are
presented later.

The use of alternative transcription start sites results in a different 5′ exon on mRNAs encoding mouse amylase and myosin light chain, rat
glucokinase, and Drosophila alcohol dehydrogenase and actin. Alternative polyadenylation sites in the μ immunoglobulin heavy­chain primary
transcript result in mRNAs that are either 2700 bases long (μm) or 2400 bases long (μs). This results in a different carboxyl­terminal region of the
encoded proteins such that the μm protein remains attached to the membrane of the B lymphocyte and the μs immunoglobulin is secreted.
Alternative splicing and processing results in the formation of seven unique α­tropomyosin mRNAs in seven different tissues. It is not yet fully
understood how these processing­splicing decisions are made or exactly how these steps can be regulated.

Regulation of Messenger RNA Stability Provides Another Control Mechanism

Although most mRNAs in mammalian cells are very stable (half­lives measured in hours), some turn over very rapidly (half­lives of 10­30 minutes). In
certain instances, mRNA stability is subject to regulation. This has important implications since there is usually a direct relationship between mRNA
amount and the translation of that mRNA into its cognate protein. Changes in the stability of a specific mRNA can therefore have major effects on
biologic processes.

Messenger RNAs exist in the cytoplasm as ribonucleoprotein particles (RNPs). Some of these proteins protect the mRNA from digestion by
nucleases, while others may under certain conditions promote nuclease attack. It is thought that mRNAs are stabilized or destabilized by the
interaction of proteins with these various structures or sequences. Certain effectors, such as hormones, may regulate mRNA stability by increasing or
decreasing the amount of these mRNA­binding proteins.

It is known that the ends of mRNA molecules are involved in mRNA stability (Figure 38–21). The 5′–cap structure in eukaryotic mRNA prevents attack
by 5′ exonucleases, and the poly(A) tail minimizes the action of 3′ exonucleases. In mRNA molecules with those structures, it is presumed that a single
endonucleolytic cut allows exonucleases to attack and digest the entire molecule. Other structures (sequences) in the 5′–untranslated region (5′ UTR),
the coding region, and the 3′ UTR are thought to promote or prevent this initial endonucleolytic action (see Figure 38–21).

FIGURE 38–21

Structure of a typical eukaryotic mRNA showing elements that are involved in regulating mRNA stability. The typical eukaryotic mRNA
has a 5′–noncoding sequence (NCS), or untranslated exonic region (5′ UTR), a coding region, and a 3′–exonic untranslated NCS region (3′ UTR).
Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186
Essentially
Chapter 38:allRegulation
mRNAs areofcapped at the 5′ end,P.
Gene Expression, and most have
Anthony Weila 100 to 200 nt polyadenylate sequence at their 3′ end. The 5′ cap and 3′ poly(A) tail
Page 31 / 33
©2025
protect McGraw
the mRNAHill. All Rights
against Reserved.
exonuclease attackTerms of Use
and are • Privacy
bound Policy
by specific • Notice
proteins that• interact
Accessibility
to facilitate translation (see Figure 37–7). Stem­loop
structures in the 5′ and 3′ NCS, and the AU­rich region in the 3′ NCS represent the binding sites for specific proteins that modulate mRNA stability.
the coding region, and the 3′ UTR are thought to promote or prevent this initial endonucleolytic action (see Figure 38–21).
Rajiv Gandhi University of Health Sciences
Access Provided by:
FIGURE 38–21

Structure of a typical eukaryotic mRNA showing elements that are involved in regulating mRNA stability. The typical eukaryotic mRNA
has a 5′–noncoding sequence (NCS), or untranslated exonic region (5′ UTR), a coding region, and a 3′–exonic untranslated NCS region (3′ UTR).
Essentially all mRNAs are capped at the 5′ end, and most have a 100 to 200 nt polyadenylate sequence at their 3′ end. The 5′ cap and 3′ poly(A) tail
protect the mRNA against exonuclease attack and are bound by specific proteins that interact to facilitate translation (see Figure 37–7). Stem­loop
structures in the 5′ and 3′ NCS, and the AU­rich region in the 3′ NCS represent the binding sites for specific proteins that modulate mRNA stability.

Thus, it is clear that a number of mechanisms are used to regulate mRNA stability and hence function—just as several mechanisms are used to regulate
the synthesis of mRNA, and as detailed in Chapter 37, mRNA translation. Coordinate regulation of these processes confers on the cell remarkable
adaptability.

SUMMARY
The genetic constitutions of metazoan somatic cells are nearly all identical.

Phenotype (tissue or cell specificity) is dictated by differences in gene expression of the cellular complement of genes.

Alterations in gene expression allow a cell to adapt to environmental changes, developmental cues, and physiologic signals.

Gene expression can be controlled at multiple levels by changes in transcription, mRNA processing, localization, and stability or translation. Gene
amplification and rearrangements also influence gene expression.

Transcription controls operate at the level of protein­DNA and protein–protein interactions. These interactions display protein domain
modularity and high specificity.

Many different structural classes of DBDs have been identified in transcription factors.

Chromatin and DNA modifications contribute importantly in eukaryotic transcription control by modulating DNA accessibility and specifying
recruitment of specific coactivators and corepressors to target genes.

Several epigenetic mechanisms for gene control have been described and the molecular mechanisms through which these processes operate are
being elucidated at the molecular level.

ncRNAs modulate gene expression. The short miRNAs and siRNAs modulate mRNA translation and stability.

REFERENCES

Ambrosi C, Manzo M, Baubec T: Dynamics and context­dependent roles of DNA methylation. J Mol Biol 2017;429(10):1459–1475. [PubMed: 28214512]

Brandao HB, Gabriele M, Hansen AS: Tracking and interpreting long­range chromatin interactions with super­resolution live­cell imaging. Curr Opin
Cell Biol 2021;70:18–26. [PubMed: 33310227]

Browning DF, Busby SJ: Local and global regulation of transcription initiation in bacteria. Nat Rev Microbiol 2016;14:638–650. [PubMed: 27498839]

Chan JC, Maze I: Nothing is yet set in (Hi)stone: novel post­transcription modifications regulating chromatin function. Trends Biochem Sci
2020;45:829–844. [PubMed: 32498971]

Chen H, Pugh BF: What do transcription factors interact with? J Mol Biol 2021; doi.org/10.1016/.mb.2021.166883.
Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186
Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 32 / 33
Dekker McGraw
©2025 J, Belmont
Hill.AS,
AllGuttman M, et al: The
Rights Reserved. 4D nucleome
Terms project. Policy
of Use • Privacy Nature•2017;549:219–278. [PubMed: 28905911]
Notice • Accessibility

Henniger E, Oksuz O, Shrinivas K, et al: RNA­mediated feedback control of transcriptional condensates. Cell 2021;184:207–225. [PubMed: 33333019]
Browning DF, Busby SJ: Local and global regulation of transcription initiation in bacteria. Nat Rev Microbiol 2016;14:638–650. [PubMed: 27498839]
Rajiv Gandhi University of Health Sciences
Access Provided by:
Chan JC, Maze I: Nothing is yet set in (Hi)stone: novel post­transcription modifications regulating chromatin function. Trends Biochem Sci
2020;45:829–844. [PubMed: 32498971]

Chen H, Pugh BF: What do transcription factors interact with? J Mol Biol 2021; doi.org/10.1016/.mb.2021.166883.

Dekker J, Belmont AS, Guttman M, et al: The 4D nucleome project. Nature 2017;549:219–278. [PubMed: 28905911]

Henniger E, Oksuz O, Shrinivas K, et al: RNA­mediated feedback control of transcriptional condensates. Cell 2021;184:207–225. [PubMed: 33333019]

Hnisz D, Abraham BJ, Lee TI, et al: Super­enhancers in the control of cell identity and disease. Cell 2013;155:934–947. [PubMed: 24119843]

Jacob F, Monod J: Genetic regulatory mechanisms in protein synthesis. J Mol Biol 1961;3:318–356. [PubMed: 13718526]

Jaeger MG, Winter GE: Fast­acting chemical tools to delineate causality in transcriptional control. Mol Cell 2021;81:1617–1630. [PubMed: 33689749]

Klug A: The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annu Rev Biochem 2010;79:213–231.
[PubMed: 20192761]

Manning KS, Cooper TA: The roles of RNA processing in translating genotype to phenotype. Nat Rev Mol Cell Biol 2017;18:102–114. [PubMed:
27847391]

Narita T, Ito S, Higashiima Y, et al: Enhancers are activated by p300/CPB activity­dependent PIC assembly, RNAPII recruitment, and pause release. Mol
Cell 2021;81:1–17. [PubMed: 33417852]

Ptashne M: A Genetic Switch , 2nd ed. Cell Press and Blackwell Scientific Publications, 1992.

Pugh BF: A preoccupied position on nucleosomes. Nat Struct Mol Biol 2010;17:923. [PubMed: 20683475]

Roeder RG: 50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms. Nat Struc Mol Biol 2019;26:783–791.

Rossi M, Kuntala PK, Lai WKM, et al: A high­resolution protein architecture of the budding yeast genome. Nature 2021;592:309–315. [PubMed:
33692541]

Schmitt AM, Chang HY: Long noncoding RNAs in cancer pathways. Cancer Cell 2016;29:452–463. [PubMed: 27070700]

Schwartzman O, Tanay A: Single­cell epigenomics: techniques and emerging applications. Nat Rev Genet 2015;16:716–726. [PubMed: 26460349]

Scotti MM, Swanson MS: RNA mis­splicing in disease. Nat Rev Genet 2016;17:19–32. [PubMed: 26593421]

Shao Q, Trinh JT, Zeng L: High­resolution studies of lysis­lysogeny decision­making in bacteriophage lambda. J Biol Chem 2019;294:3343–3349.
[PubMed: 30242122]

Tee WW, Reinberg D: Chromatin features and the epigenetic regulation of pluripotency states in ESCs. Development 2014;141:2376–2390. [PubMed:
24917497]

Tian B, Manley JL: Alternative polyadenylation of mRNA precursors. Nat Rev Mol Cell Biol 2017;18:18–30. [PubMed: 27677860]

Wang Z, Cairns MJ, Yan J: Super­enhancers in transcriptional regulation and genome organization. Nuc Acids Res 2019:11481–11496.

Wang Z, Cui M, Shah AM, et al: Cell­type­specific gene regulatory networks underlying murine neonatal heart regeneration at single­cell resolution.
Cell Reports 2020;33:108472. [PubMed: 33296652]

Zaborowska J, Egloff S, Murphy S: The pol II CTD: new twists in the tail. Nat Struct Mol Biol 2016;23:771–777. [PubMed: 27605205]

Downloaded 2025­5­17 3:44 P Your IP is 13.233.228.186

Chapter 38: Regulation of Gene Expression, P. Anthony Weil Page 33 / 33
©2025 McGraw Hill. All Rights Reserved. Terms of Use • Privacy Policy • Notice • Accessibility