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GENE EXPRESSION AND REGULATION | Lead Editor: Laura Hoopes

Regulation of Transcription and Gene Expression in

Eukaryotes
By: Theresa Phillips, Ph.D. (Write Science Right) © 2008 Nature Education
Citation: Phillips, T. (2008) Regulation of transcription and gene expression
in eukaryotes. Nature Education 1(1):199

If our genes are so similar, what really makes a eukaryote di!erent from a prokaryote, or a human from E.
coli? The answer lies in the di!erence in gene expression and regulation used.
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It is estimated that the human genome encodes approximately 25,000 genes, about the same number as that for corn and nearly twice as many as that for the common fruit fly.
Even more interesting is the fact that those 25,000 genes are encoded in about 1.5% of the genome. So, what exactly does the other 98.5% of our DNA do? While many mysteries
remain about what all of that extra sequence is for, we know that it does contain complex instructions that direct the intricate turning on and o! of gene transcription.

Eukaryotes Require Complex Controls Over Gene Expression

While basic similarities in gene transcription exist between prokaryotes and eukaryotes—including the fact that RNA polymerase binds upstream of the gene on its promoter to
initiate the process of transcription—multicellular eukaryotes control cell di!erentiation through more complex and precise temporal and spatial regulation of gene expression.

Multicellular eukaryotes have a much larger genome than prokaryotes, which is organized into multiple chromosomes with greater sequence complexity. Many eukaryotic
species carry genes with the same sequences as other plants and animals. In addition, the same DNA sequences (though not the same proteins) are found within all of an
organism's diploid, nucleated cells, even though these cells form tissues with drastically di!erent appearances, properties, and functions. Why then, is there such great variation
among and within such organisms? Quite simply, the way in which di!erent genes are turned on and o! in specific cells generates the variety we observe in nature. In other
words, specific functions of di!erent cell types are generated through di!erential gene regulation.

Of course, higher eukaryotes still respond to environmental signals by regulating their genes. But there is an additional layer of regulation that results from cell-to-cell
interactions within the organism that orchestrate development. Specifically, gene expression is controlled on two levels. First, transcription is controlled by limiting the amount
of mRNA that is produced from a particular gene. The second level of control is through post-transcriptional events that regulate the translation of mRNA into proteins. Even
after a protein is made, post-translational modifications can a!ect its activity.

Transcriptional Regulation in Eukaryotes

Regulation of transcription in eukaryotes is a result of the combined e!ects of structural properties (how DNA is "packaged") and the interactions of proteins called transcription
factors. The most important structural di!erence between eukaryotic and prokaryotic DNA is the formation of chromatin in eukaryotes. Chromatin results in the di!erent
transcriptional "ground states" of prokaryotes and eukaryotes (Table 1).

Table 1: Overview of Di!erences Between Prokaryotic and Eukaryotic Gene Expression and Regulation

Prokaryotes Eukaryotes

Structure of genome Single, generally circular Genome found in

genome sometimes chromosomes; nucleosome
accompanied by smaller structure limits DNA
pieces of accessory DNA, accessibility
like plasmids

Size of genome Relatively small Relatively large

Location of gene Coupled; no nucleoid Nuclear transcription and
transcription and envelope barrier because cytoplasmic translation
translation of prokaryotic cell
structure
Gene clustering Operons where genes Operons generally not
with similar function are found in eukaryotes; each
grouped together gene has its own
 promoter element and
enhancer element(s)

Default state of On O!
transcription
DNA structure Highly supercoiled DNA Highly supercoiled
with some associated chromatin associated with
proteins histones in nucleosomes

Transcription Factors and Combinatorial Control

Transcription factors (TFs) are regulatory proteins whose function is to activate (or more rarely, to inhibit)
transcription of DNA by binding to specific DNA sequences. TFs have defined DNA-binding domains with up
to 106-fold higher a"nity for their target sequences than for the remainder of the DNA strand. These highly
conserved sequences have been used to categorize the known TFs into various "families," such as the MADS
box-containing proteins, SOX proteins, and POU factors (Remenyi et al., 2004). Transcription factors can
also be classified by their three-dimensional protein structure, including basic helix-turn-helix, helix-loop-
helix, and zinc finger proteins. These di!erent structural motifs result in transcription factor specificity for
the consensus sequences to which they bind.

Sequence-specific transcription factors are considered the most important and diverse mechanisms of gene
regulation in both prokaryotic and eukaryotic cells (Pulverer, 2005). In eukaryotes, regulation of gene
expression by transcription factors is said to be combinatorial, in that it requires the coordinated interactions
of multiple proteins (in contrast to prokaryotes, in which a single protein is usually all that is required).

Many genes, known as housekeeping genes, are needed by almost every type of cell and appear to be
unregulated or constitutive. But at the core of cellular di!erentiation, manifested in the variety of cell types
observed in di!erent organisms, is the regulation of gene expression in a tissue-specific manner. The same Figure 1: DNA footprinting reveals transcription
genome is responsible for making the entire cadre of cell types, each of which has its own function—for factor specificity in di!erent cell types
example, red blood cells exchange oxygen, muscle cells expand and contract, and cells in the immune In vivo footprinting analysis of the human beta globin
system recognize pathogens. Genes that regulate cell identity are turned on under very specific temporal, promoter shows that adult erythroblasts (E, lane 4) have
spatial, and environmental conditions to ensure that a cell is able to perform its designated function. footprints on important regulatory motifs (note lighter
regions, especially at CACC) as compared to the other
Take the example of the gene for beta globin, a protein used in red blood cells for oxygen exchange. Every
samples. Here, lane N is control DNA, lane H is HeLa cells,
cell in the human body contains the beta globin gene and the corresponding upstream regulatory sequences
lane K is K562 cells, lane R is Raji cells, and lane J is Jurkat
that regulate expression, but no cell type other than red blood cells expresses beta globin. Scientists can use
cells. Of these cells lines, none is part of the lineage
a technique called DNA footprinting to map where transcription factors bind to specific regulatory sequences.
leading to red blood cells.
When Reddy et al. examined the beta globin promoter in di!erent cell types, they found that the transcription
© 1994 American Society for Biochemistry and
factors that could bind to the promoter sequences required for beta globin expression were expressed only in
Molecular Biology Reddy, P. M. et al. Genomic
erythroblasts (immature adult red blood cells). (See Figure 1). The two consensus sequences in the beta
footprinting and sequencing of human beta-globin locus:
globin promoter known for binding transcription factors, CCAAT and CACC, were protected in the erythroid
tissue specificity and cell line artifact. Journal of Biological
cells (E), but not the other cell types (Reddy et al., 1994).
Chemistry 269, 8287–8295 (1994). All rights reserved.

The "Ground State" of DNA Expression

RNA polymerase in prokaryotes can access almost any promoter in a DNA strand without the presence of activators or repressors. Thus, the "ground state" of DNA expression in
prokaryotes is said to be nonrestrictive, or "on." In eukaryotes, however, the ground state of expression is restrictive in that, although strong promoters might be present, they
are inactive in the absence of some sort of recruitment to the promoter by transcription factors. For instance, RNA polymerase II, which transcribes mRNA, cannot bind to
promoters in eukaryotic DNA without the help of transcription factors (Struhl, 1999). In many eukaryotic organisms, the promoter contains a conserved gene sequence called the
TATA box. Various other consensus sequences also exist and are recognized by the di!erent TF families. Transcription is initiated when one TF binds to one of these promoter
sequences, initiating a series of interactions between multiple proteins (activators, regulators, and repressors) at the same site, or other promoter, regulator, and enhancer
sequences. Ultimately, a transcription complex is formed at the promoter that facilitates binding and transcription by RNA polymerase.

As in prokaryotes, eukaryotic repressor molecules can sometimes bind to silencer elements in the vicinity of a gene and inhibit the binding, assembly, or activity of the
transcription complex, thus turning o! expression of a gene. Positive regulation by TFs that are activators is common in eukaryotes. Considering the restrictive transcriptional
ground state, it is logical that positive regulation is the predominant form of control in all systems characterized to date. Many activating TFs are generally bound to DNA until
removed by a signal molecule, while others might only bind to DNA once influenced by a signal molecule. The binding of one type of TF can influence the binding of others, as
well. Thus, gene expression in eukaryotes is highly variable, depending on the type of activators involved and what signals are present to control binding.

The Role of Chromatin

Even when transcription factors are present in a cell, transcription does not always occur, because often the TFs cannot reach their target sequences. The association of the DNA
molecule with proteins is the first step in its silencing. The associated DNA and histone proteins are collectively called chromatin; the complex is tightly bonded by attraction of
the negatively charged DNA to the positively charged histones (Table 1). The state of chromatin can limit access of transcription factors and RNA polymerase to DNA promoters,
contributing to the restrictive ground state of gene expression. In order for gene transcription to occur, the chromatin structure must be unwound.

Chromatin structure contributes to the varying levels of complexity in gene regulation. It allows simultaneous regulation of functionally or structurally related genes that tend to
be present in widely spaced clusters or domains on eukaryotic DNA (Sproul et al., 2005). Interactions of chromatin with activators and repressors can result in domains of
chromatin that are open, closed, or poised for activation. Chromatin domains have various sizes and di!erent extents of stability. These variations allow for phenomena found
solely in eukaryotes, such as transcription at various stages of development and epigenetic memory throughout cell division cycles. They also allow for the maintenance of
di!erentiated cellular states, which is crucial to the survival of multicellular organisms (Struhl, 1999).

Multiple Interactions Provide Synchronous Control

As you have seen, the state of chromatin structure at a specific region in eukaryotic DNA, along with the presence of specific transcription factors, works to regulate gene
expression in eukaryotes. However, this complex interplay between proteins that serve as transcriptional activators or repressors and accessibility to the regulatory sequence is
still just part of the story. Epigenetic mechanisms, including DNA methylation and imprinting, noncoding RNA, post-translational modifications, and other mechanisms, further
enrich the cellular portfolio of gene expression control activities.

References and Recommended Reading

Pulverer, B. Sequence-specific DNA-binding transcription factors. Nature Milestones (2005) doi: 10.1038/nrm1800 (link to article)

Reddy, P. M., Stamatoyannopoulos, G., Papayannopoulou, T., & Shen, C. K. Genomic footprinting and sequencing of human beta-globin locus: Tissue specificity and cell line
artifact. Journal of Biological Chemistry 269, 8287–8295 (1994)

Remenyi, A., Scholer, H., & Wilmanns, M. Combinatorial control of gene expression. Nature Structural and Molecular Biology 11, 812–815 (2004) doi:10.1038/nsmb820 (link

to article)

Struhl, K. Fundamentally di!erent logic of gene regulation in eukaryotes and prokaryotes. Cell 98, 1–4 (1999)

Sproul, D., Gilbert, N., & Bickmore, W. The role of chromatin structure in regulating the expression of clustered genes. Nature Reviews Genetics 6, 775–781 (2005)

doi:10.1038/nrg1688 (link to article)

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