5.

3 Eukaryotic Gene Regulation

Learning Objectives

By the end of this section, you will be able to:

 Explain the process of epigenetic gene regulation in eukaryotic cells.

 Explain the process of transcriptional gene regulation in eukaryotic cells.
 Explain the process of post-transcriptional gene regulation in eukaryotic cells.
 Explain the process of translational gene regulation in eukaryotic cells.
 Explain the process of post-transcriptional gene regulation in eukaryotic cells.

In eukaryotes, control of gene expression is more complex and can happen at many different
levels. Eukaryotic genes are not organized into operons, so each gene must be regulated
independently. In addition, eukaryotic cells have many more genes than prokaryotic cells.
Regulation of gene expression can happen at any of the stages as DNA is transcribed into mRNA
and mRNA is translated into protein. For convenience, regulation is divided into five levels:
epigenetic, transcriptional, post-transcriptional, translational, and post-translational (Figure
17.6).

Figure 17.6 Regulation of gene expression in eukaryotes can occur at five different levels. Here,
the Central Dogma is diagrammed with arrows showing where each type of eukaryotic
regulation of gene expression interrupts it.

17.3.1 Epigenetic Control fo Gene Expression

The first level of control of gene expression is epigenetic (“around genetics”) regulation.
Epigenetics is a relatively new, but growing, field of biology.

Epigenetic control involves changes to genes that do not alter the nucleotide sequence of the
DNA and are not permanent. Instead, these changes alter the chromosomal structure so that
genes can be turned on or off. This level of control occurs through heritable chemical
modifications of the DNA and/or chromosomal proteins.
One example of chemical modifications of DNA is the addition of methyl groups to the DNA, in
a process called methylation, In general, methylation suppresses transcription. Interestingly,
methylation patterns can be passed on as cells divide. Thus, parents may be able to pass on the
tendency of a gene to be expressed in their offspring. Other heritable chemical modifications of
DNA may also occur.

Modification of Histone Proteins is an Example of Epigenetic Control

The best-studied example of epigenetic regulation is modification of histone proteins. Histones

are chromosomal proteins that tightly wind DNA so that it fits into the nucleus of a cell. The
human genome, for example, consists of over three billion nucleotide pairs. An average
chromosome contains 130 million nucleotide pairs, and each body cell contains 46
chromosomes. If stretched out linearly, an average human chromosome would be over four
centimeters long. In order to fit all of this DNA into the nucleus of a microscopic cell, the DNA
must be tightly wound around proteins. It is also organized so that specific segments can be
accessed as needed by a specific cell type (Figure 17.7).

Figure 17.7 In each

chromosome, DNA is wound around histone proteins to pack it into the nucleus of a cell. (Credit:
modification of work by NIH.)
The first level of organization, or packing, is the winding of DNA strands around histone
proteins. Histones package and order DNA into structural units called nucleosome complexes,
which can control the access of proteins to the DNA regions (Figure 17.8a). Under the electron
microscope, this winding of DNA around histone proteins to form nucleosomes looks like small
beads on a string (Figure 17.8b). These beads (histone proteins) can move along the string
(DNA) and change the structure of the molecule.

Figure 17.8 DNA is wrapped

around histones to create nucleosomes (a), which control the access of proteins to DNA. When
viewed through an electron microscope (b), the nucleosomes look like beads on a string. (Credit
“micrograph”: modification of work by Chris Woodcock.)

If a gene is to be transcribed, the nucleosomes surrounding that region of DNA can slide down
the DNA to open that specific chromosomal region and allow access for RNA polymerase and
other proteins, called transcription factors, to bind to the promoter region and initiate
transcription. If a gene is to remain turned off, or silenced, the histone proteins and DNA have
different modifications that signal a closed chromosomal configuration. In this closed
configuration, the RNA polymerase and transcription factors do not have access to the DNA and
transcription cannot occur (Figure 17.9).

How the histone proteins move is dependent on signals found on the histone proteins. These
signals are “tags” – in the form of phosphate, methyl, or acetyl groups – that open or close a
chromosomal region (Figure 17.9). These tags are not permanent, but may be added or removed
as needed. Since DNA negatively charged, changes in the charge of the histone will change how
tightly wound the DNA molecule will be. When unmodified, the histone proteins have a large
positive charge; by adding chemical modifications like acetyl groups, the charge becomes less
positive.
 Figur
e 17.9 Nucleosomes can slide along DNA. (A) When nucleosomes are spaced closely together,
transcription factors cannot bind and gene expression is turned off. (B) When nucleosomes are
spaced far apart, transcription factors can bind, allowing gene expression to occur.

17.3.2 Transcriptional Control of Gene Expression

Transcriptional regulation is control of whether or not an mRNA is transcribed from a gene in
a particular cell. Like prokaryotic cells, the transcription of genes in eukaryotes requires an RNA
polymerase to bind to a promoter to initiate transcription. In eukaryotes, RNA polymerase
requires other proteins, or transcription factors, to facilitate transcription initiation.
Transcription factors are proteins that bind to the promoter sequence and other regulatory
sequences to control the transcription of the target gene. RNA polymerase by itself cannot
initiate transcription in eukaryotic cells. Transcription factors must bind to the promoter region
first and recruit RNA polymerase to the site for transcription to begin.

The Promoter and Transcription Factors

In eukaryotic genes, the promoter region is immediately upstream of the coding sequence. This
region can range from a few to hundreds of nucleotides long. The length of the promoter is gene-
specific and can differ dramatically between genes. The longer the promoter, the more available
space for proteins to bind. Consequently, the level of control of gene expression can differ quite
dramatically between genes. The purpose of the promoter is to bind transcription factors that
control the initiation of transcription (Figure 17.10, top).

Within the promoter region, just upstream of the transcriptional start site, resides the TATA box.
This box is simply a repeat of thymine and adenine dinucleotides (literally, TATA repeats).
Transcription factors bind to the TATA box, assembling an initiation complex. Once this
complex is assembled, RNA polymerase binds to its upstream sequence and becomes
phosphorylated. This releases part of the protein from the DNA, activates the transcription
initiation complex, and places RNA polymerase in the correct orientation to begin transcription
(Figure 17.10, top).

Figure 17.10 Top. Each gene has a promoter upstream of the coding sequence. The promoter
binds to transcription factors and helps RNA polymerase to bind and start transcription. Bottom.
Many genes also have upstream enhancers. Enhancers bind activators, bend around, and help
RNA polymerase start transcription.

Enhancers and Repressors

In some eukaryotic genes, there are regions that help increase transcription. These regions, called
enhancers, are not necessarily close to the genes; they can be located thousands of nucleotides
away. They can be found upstream, within the coding region, or downstream of a gene.
Enhancers are binding sites for activators. When an enhancer is far away from a gene, the DNA
folds such that the enhancer is brought into proximity with the promoter, allowing interaction
between the activators and the transcription initiation complex (Figure 17.10, bottom).

Like prokaryotic cells, eukaryotic cells also have mechanisms to prevent transcription.
Transcriptional repressors can bind to promoter or enhancer regions and block transcription.
Both activators and repressors respond to external stimuli to determine which genes need to be
expressed.

17.3.3 Post-transcriptional Control of Gene Expression

Post-transcriptional regulation occurs after the mRNA is transcribed but before translation
begins. This regulation can occur at the level of mRNA processing, transport from the nucleus to
the cytoplasm, or binding to ribosomes.

Alternative RNA splicing

Recall from chapter 5 that in eukaryotic cells the RNA primary transcript often contains introns,
which are removed prior to translation.

Alternative RNA splicing is a mechanism that allows different combinations of introns, and
sometimes exons, to be removed from the primary transcript (Figure 17.11). This allows
different protein products to be produced from one gene. Alternative splicing can act as a
mechanism of gene regulation. Differential splicing is used to produce different protein products
in different cells or at different times within the same cell. Alternative splicing is now
understood to be a common mechanism of gene regulation in eukaryotes; up to 70 percent of
genes in humans are expressed as multiple proteins through alternative splicing.

Figure
17.11 Before a RNA can be translated, introns must be removed by splicing. Pre-mRNA can be
alternatively spliced to create different proteins.

Evolution of Alternative Splicing

How could alternative splicing evolve? Introns have a beginning and ending recognition
sequence; it is easy to imagine the failure of the splicing mechanism to identify the end of an
intron and instead find the end of the next intron, thus removing two introns and the intervening
exon. In fact, there are mechanisms in place to prevent such intron skipping, but mutations are
likely to lead to their failure. Such “mistakes” would more than likely produce a nonfunctional
protein. Indeed, the cause of many genetic diseases is alternative splicing rather than mutations
in a sequence. However, alternative splicing would create a protein variant without the loss of
the original protein, opening up possibilities for adaptation of the new variant to new functions.
Gene duplication has played an important role in the evolution of new functions in a similar way
by providing genes that may evolve without eliminating the original, functional protein.

Control of RNA Stability

Another type of post-transcriptional control involves the stability of the mRNA in the cytoplasm.
The longer an mRNA exists in the cytoplasm, the more time it has to be translated, and the more
protein is made. Many factors contribute to mRNA stability, including the length of its poly-A
tail.

Figure
17.12 The protein-coding region of mRNA is flanked by 5′ and 3′ untranslated regions (UTRs).
RNA-binding proteins at the 5′ or 3′ UTR influence the stability of the RNA molecule.

Proteins, called RNA-binding proteins (RBPs) can bind to the regions of the RNA just upstream
or downstream of the protein-coding region. These regions in the RNA that are not translated
into protein are called the untranslated regions, or UTRs. The region just before the protein-
coding region is called the 5′ UTR, whereas the region after the coding region is called the 3′
UTR (Figure 17.12). The binding of RBPs to these regions can increase or decrease the stability
of an RNA molecule, depending on the specific RBP that binds.

microRNAs, or miRNAs, can also bind to the RNA molecule. miRNAs are short (21–24
nucleotides) RNA molecules that are made in the nucleus as longer pre-miRNAs and then
chopped into mature miRNAs by a protein called dicer. miRNAs bind to mRNA along with a
ribonucleoprotein complex called the RNA-induced silencing complex (RISC). The RISC-
miRNA complex rapidly degrades the target mRNA.

17.3.4 Translational Control of Gene Expression

After an mRNA has been transported to the cytoplasm, it is translated into proteins. Control of
this process is largely dependent on the mRNA molecule. As previously discussed, the stability
of the mRNA will have a large impact on its translation into a protein. Translation can also be
regulated at the level of binding of the mRNA to the ribosome. Once the mRNA bound to the
ribosome, the speed and level of translation can still be controlled. An example of translational
control occurs in proteins that are destined to end up in an organelle called the endoplasmic
reticulum (ER). The first few amino acids of these proteins are a tag called a signal sequence. As
soon as these amino acids are translated, a signal recognition particle (SRP) binds to the signal
sequence and stops translation while the mRNA-ribosome complex is shuttled to the ER. Once
they arrive, the SRP is removed and translation resumes.

17.3.5 Post-translational Control of Gene Expression

The final level of control of gene expression in eukaryotes is post-translational regulation.
This type of control involves modifying the protein after it is made, in such as way as to affect
its activity. One example of post-translational regulation is enzyme inhibition. When an enzyme
is no longer needed, it is inhibited by a competitive or allosteric inhibitor, which prevents it from
binding to its substrate. The inhibition is reversible, so that the enzyme can be reactivated later.
This is more efficient than degrading the enzyme when it is not needed and then making more
when it is needed again.

The activity and/or stability of proteins can also be regulated by adding functional groups, such
as methyl, phosphate, or acetyl groups. Sometimes these modifications can regulate where a
protein is found in the cell—for example, in the nucleus, the cytoplasm, or attached to the
plasma membrane.

The addition of an ubiquitin group to a protein marks that protein for degradation. Ubiquitin
acts like a flag indicating that the protein’s lifespan is complete. Tagged proteins are moved to a
proteasome, an organelle that degrades proteins (Figure 17.13). One way to control gene
expression, therefore, is to alter the longevity of the protein.
 Figure
17.13 Proteins with ubiquitin tags are marked for degradation within the proteasome.

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