Chapter 4 Regulation of Gene Expression 04 CSLS / THE UNIVERSITY OF TOKYO 67 Part I Relationship between Cells and Genetic Information Chapter 4 Regulation of Gene Expression A bacteria Escherichia coli has approximately 4,300 genes, while human cells have around 26,000. These genes are not always expressed, and their expression is regulated. Those essential for the sustenance and multiplication of cells are collectively referred to as housekeeping genes. Unicellular prokaryotes such as E. coli and multicellular eukaryotes such as humans have similar mechanisms in gene expression control. Multicellular eukaryotes also have genes associated with cell differentiation. A eukaryote-specific structure known as chromatin plays an important role in gene regulation for such function. Heterochromatin is a tightly packed form of chromatin in which gene expression is limited, while euchromatin – a loosely packed form of chromatin – has genes that are under active transcription. Chromatin structure also affects gene expressions, by changing its structure according to variable cell environment. I. Gene Types in Terms of Expression The Function of Housekeeping Genes in All Organisms Housekeeping genes are essential for the sustenance and multiplication of cells, and include genes associated with energy production, intermediary metabolism of sugars, lipids, amino acids, etc., and biosynthesis of nucleic acids and proteins. The functions performed by housekeeping genes mean they can also be thought of as vital genes. Needless to say, those necessary for survival differ between autotrophs (organisms that can produce organic compounds from inorganic molecules – such as plants) and heterotrophs (organisms that ingest organic compounds as food – such as animals). Additional Gene Function in Multicellular Organisms Multicellular organisms such as humans have many types of differentiated cells, and each cell has specific gene expression patterns for each of diverse cell
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Chap t e r 4 R eg u l a t i o n o f Gene E xp r e s s i o n
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Part I
Relationship between Cells and Genetic Information
Chapter 4Regulation of Gene Expression
A bacteria Escherichia coli has approximately 4,300 genes, while human cells
have around 26,000. These genes are not always expressed, and their
expression is regulated. Those essential for the sustenance and multiplication of
cells are collectively referred to as housekeeping genes. Unicellular prokaryotes
such as E. coli and multicellular eukaryotes such as humans have similar
mechanisms in gene expression control. Multicellular eukaryotes also have genes
associated with cell differentiation. A eukaryote-specific structure known as
chromatin plays an important role in gene regulation for such function.
Heterochromatin is a tightly packed form of chromatin in which gene expression
is limited, while euchromatin – a loosely packed form of chromatin – has genes
that are under active transcription. Chromatin structure also affects gene
expressions, by changing its structure according to variable cell environment.
I . Gene Types in Terms of Expression
The Function of Housekeeping Genes in All Organisms
Housekeeping genes are essential for the sustenance and multiplication of cells,
and include genes associated with energy production, intermediary metabolism
of sugars, lipids, amino acids, etc., and biosynthesis of nucleic acids and
proteins. The functions performed by housekeeping genes mean they can also be
thought of as vital genes. Needless to say, those necessary for survival differ
between autotrophs (organisms that can produce organic compounds from
inorganic molecules – such as plants) and heterotrophs (organisms that ingest
organic compounds as food – such as animals).
Additional Gene Function in Multicellular Organisms
Multicellular organisms such as humans have many types of differentiated cells,
and each cell has specific gene expression patterns for each of diverse cell
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functions. Humans are said to consist of some 200 types of cell. Skin cells, liver
cells and nerve cells, among others, have different shapes and functions because
different sets of genes are expressed in each of them. As an example, the serum
albumin gene is expressed only in hepatocytes, while the insulin gene is expressed
only in pancreatic β-cells. These genes are not expressed in other cells. For
multiple cells to form an organism, gene functions that are not required in
unicellular organisms become essential. Such functions include cell adhesion on
a micro level and the organization of connective tissue*1 on a macro level.
Genes associated with intercellular signaling pathway– i.e., those involved in the
biological regulation of an organism – are also necessary. Thus, many of the
genes essential for the survival of multicellular organisms are expressed only in
certain cell types or at certain stages of development.
The Identical Nature of All Somatic Cells from a Particular Individual
While each differentiated cell expresses a unique set of genes, all somatic cells
that make up an individual are believed to share the same two sets of genes, one
inherited from each parent. Although this is difficult to prove, in the plant kingdom
it has long been known that a clone plant body can be produced from a single
somatic cell, and cloned animals from several mammal species have recently
been successfully created from single somatic cells. This indicates that a gene set
housed in a single somatic cell is capable of creating all cells that make up an
organism (including somatic cells*2 and germ cells). While this has not been
confirmed in humans, it is assumed that we are not an exception. Differentiated
cells in which different sets of genes are expressed do exist, despite the assumption
that all somatic cells have the same gene sets, because mechanisms are in action
to regulate gene expression.
Genes Subject to and Free of Expression
Genes involved in energy metabolism and protein synthesis in cells must act
continuously to maintain the life of those cells. This constant gene expression is
called constitutive expression. On the other hand, situational expression of genes
is called regulated expression. Very roughly speaking, housekeeping genes
include those that express constitutively; however, even genes for enzymes
involved in energy metabolism often change their expression levels according to
cell environments, and the expression of genes involved in proliferation is
*1Connective tissue: A type of tissue with a rich extracellular matrix (see Chapter 11). Connects cells and tissues and, as a frame, maintains the shape and strength of an animal’s body.
*2Somatic cells: All cells other than germ cells in multicellular organisms are called somatic cells. Most of the cells that make up an organism are therefore somatic cells.
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suppressed during growth arrest.
It is clear that at least two expression regulation mechanisms exist for genes that
are involved in differentiation functions. One is the mechanism in which, among
the various cells in the body, only β-cells in the pancreas express insulin genes
while other cells do not. The other is the mechanism of β-cells, in which the
expression level of insulin genes is increased when blood sugar rises and is
reduced when it falls. These two regulation mechanisms are found in the
differentiation functions not only of β-cells but of all cells.
Lymphocytes – the Only Cells with Different Genes
All human somatic cells except lymphocytes have the same genes. Humans
can produce hundreds of millions of antibody types (proteins). However,
although we have an enormous number of genes, all our somatic cells have
only precursors of antibody genes, which cannot produce antibody proteins.
During the differentiation process of lymphocytes, recombination occurs in
antibody genes, thereby equipping each lymphocyte with just one antibody
gene. As a result, a single human has genes to produce hundreds of millions
of antibody types, whereas each lymphocyte has a gene for only one
antibody type. If a clone is made from a lymphocyte, the clone will be able
to synthesize only one antibody type (or may not be able to synthesize
antibodies at all).
I I . Gene Expression Regulation in Prokaryotes
Positive and Negative Regulation of the β-galactosidase Gene in E. Coli
The mechanism of gene expression regulation was first revealed in the
β-galactosidase gene. This mechanism represents the basic functions of gene
expression and suppression.
E. coli cannot directly use lactose (see Fig. 1-5 in Chapter 1), but can do so by
hydrolyzing it to glucose using the β-galactosidase enzyme. E. coli bacteria
cultured in a medium containing glucose do not produce the β-galactosidase
Column
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enzyme (the β-galactosidase gene does not function), but if the medium contains
lactose instead, they are able to use this lactose by producing the β-galactosidase
protein. This mechanism, which may sound rather simple, has another characteristic;
the presence of lactose does not mean the production of the β-galactosidase
enzyme if glucose is also present. It is very reasonable that the β-galactosidase
protein is synthesized only when lactose is present and glucose is not.
This regulation mechanism is shown in Figures 4-1 and 4-2. The operator
sequence lies in the upstream promoter region of the β-galactosidase gene. A
protein constitutively produced by the lac i gene (known as a repressor) binds to
the operator region, thus suppressing the action of RNA polymerase. This is the
negative regulation of the β-galactosidase gene (Fig. 4-1). Under the presence
of lactose, allolactose – a derivative of lactose – binds to the repressor protein
and deprives it of repressor functions, thus preventing it from binding to the
operator. Therefore, if RNA polymerase can bind to the promoter in the presence
of lactose, mRNA can be synthesized from the β-galactosidase gene.
In lactose operon system, RNA polymerase can bind to the promoter only after
the cAMP-CRP complex (i.e., a complex in which cAMP (3’, 5’-cyclic AMP) binds
to CRP*3 (or CAP)) has bound to the promoter. This constitutes positive regulation
of the β-galactosidase gene (Fig. 4-2). The expression of this gene is suppressed
in the presence of glucose because the transport of lactose into the cell is
absolutely inhibited, which disables the production of allolactose, thus keeping
the repressor from being detached from the operator.
In summary, there are positive- and negative-regulation proteins in gene
regulations, each of which binds to the promoter region of a gene, thus regulating
its transcription. Similar regulation mechanisms can be found not only in the
utilization of carbohydrates such as arabinose, but also in genes that are involved
in the metabolism of amino acids and other substances.
*3CRP: CRP (cAMP receptor protein) is a type of transcriptional regulation factor that binds to the promoter after binding to cAMP, allowing RNA polymerase to bind to the promoter and thereby positively regulating RNA synthesis.
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Figure 4-1 Negative regulation by a repressor
Figure 4-2 Positive regulation by CRP*3
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E. coli bacteria have genes for enzymes that synthesize all amino acids,
carbohydrates, lipids and nucleic acids from ammonia and glucose, thus
regulating gene expression as necessary. As an example, when an amino
acid called histidine is present in a medium, E. coli suppress all ten enzyme
genes involved in histidine synthesis; when histidine is absent, E. coli
simultaneously expresses these ten genes. In the case of the β-galactosidase
gene, three related genes are simultaneously expressed and suppressed.
These are located alongside each other in the DNA, and mRNA that reads
these genes successively is synthesized. In other words, one mRNA molecule
contains information on multiple genes. Such molecules are known as
polycistronic mRNA (Column Fig. 4-1). The term “cistron” is synonymous
with genes. An operon is a gene unit controlled by one region of gene
expression regulation (i.e., one operator), and examples include lactose
operons and histidine operons. Generally, in association with the synthesis
and utilization of nutrients, prokaryotes have many gene regulation
mechanisms that are sophisticated to fulfill their intended purposes. In this
mechanism, a large number of genes form operons to generate polycistronic
mRNA. Each coding region in polycistronic mRNA is bound with a ribosome,
thereby synthesizing proteins. However, eukaryotes do not have operons,
and therefore do not produce polycistronic mRNA.
Column Mechanism of Simultaneously Regulating the Expression of Multiple Genes
Column Figure 4-1 Comparison of mRNA structure between prokaryotes and eukaryotes
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I I I . Regulation of Gene Expression in Eukaryotic Cells
Transcriptional and Posttranscriptional Regulations
In prokaryotes, a ribosome binds to mRNA that is still being synthesized and
initiates protein synthesis, and the mRNA is degraded with a half-life of a few
minutes (see Fig. 3-14 in Chapter 3). Determination of whether a gene is
expressed to synthesize a protein is mainly based on whether mRNA is transcribed
from it, or in other words, by transcriptional regulation.
In eukaryotes, on the other hand, mRNA is first transcribed as pre-mRNA (i.e.,
precursor mRNA), which, after going through various processes in the nucleus, is
transported to the cytoplasm through the nuclear pores, where it is used for protein
synthesis (Fig. 4-3). The transcriptional regulation of mRNA is also essential in
eukaryotes (as discussed later in more detail), and the process between
transcription and protein synthesis is also regulated. Regulation after transcription
is called posttranscriptional regulation, and one of the characteristics of
eukaryotic cells is that they are subject to posttranscriptional regulation in addition
to transcriptional regulation.
Figure 4-3 Transcription and translation in eukaryotes
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With regard to posttranscriptional regulation, it is known that the stages of
splicing, transportation from the nucleus to the cytoplasm, translation in the
cytoplasm and mRNA degradation vary with the developmental stage in the
same cell, as well as exhibiting specificity depending on the tissue and cell and
changing in line with the in vivo physiological conditions. It is also known that
pre-mRNA molecules made from the same gene have different destinies in
different cells, which leads to the production of proteins with different amino
acid sequences.
In prokaryotes, the use of operons is not the only means of simultaneously
regulating multiple genes. As an example, when heat shock is applied to
prokaryotes through high temperature, unusual transcription initiation factors
are produced, which induces the expression of multiple genes for proteins
called heat shock proteins, thus causing response reactions to the heat
shock. Heat shock protein genes do not form operons, and are spread over
the DNA. The mechanism that simultaneously regulates the expression of
such scattered genes is called a regulon (a heat shock regulon in the case
of the example above). Likewise, the SOS regulon induces the expression of
many DNA repair enzymes when DNA has been damaged.
Column Operons and Regulons
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Gene Expression Regulation by miRNA
It is mentioned earlier in this book that rRNA and tRNA are the main classes
of non-coding RNA, and are found in all cells, but eukaryotes also have
snRNA (a type of non-coding RNA), which is involved in splicing (see III in
Chapter 3). It has recently been discovered that small RNA molecules
suppress gene expression (Column Fig. 4-2). Such RNA is believed to inhibit
transcription by sequence-specifically binding to DNA, binding to and
degrading mRNA and inhibiting protein synthesis. The phenomenon of gene
expression interference by RNA is called RNAi (RNA interference). RNA
molecules with such functions all belong to the non-coding RNA group. RNA
that acts on mRNA is synthesized as complementary double-stranded RNA
or hairpin RNA, which is cut into small fragments (approx. 21 bp) by double
strand RNA cleaving enzymes (i.e., dicers), and functions after binding to
a protein complex called RISC. These small RNA molecules are called
miRNA (micro RNA), and inhibit protein synthesis only for specific mRNA. If
such RNA is experimentally introduced to a cell (or synthesized in a cell) it
acts as siRNA (small interfering RNA), with effects similar to those seen when
gene function is knocked out. This method is therefore called knockdown,
and is now widely used in research.
Column
Column Figure 4-2 Gene expression regulation by miRNA
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Eukaryotes with a More Complex Transcriptional Regulation Mechanism
Eukaryotic genes also have a promoter region to which RNA polymerase binds.
The basic mechanism of this binding in eukaryotes is similar to that in prokaryotes,
but is far more complicated. Eukaryotes have many proteins that recognize
particular sequences (called general transcription factors), and these proteins
bind to RNA polymerase to bring about its binding to the promoter (Fig. 4-4).
Particular DNA sequences involved in transcriptional regulation, including the
promoter, are called cis-elements, and the proteins that bind to these elements to
regulate their expression (Fig. 4-5) are trans-elements.
In addition to these basic mechanisms, some genes have transcriptional regulatory
sequences called enhancers and silencers to enable changes in their expression
in response to developments in intra- and extracellular conditions. These regions
are cis-elements with specific sequences, and some proteins recognize and bind
to them (these are known as trans-elements). The specific binding proteins to the
enhancer sequence promote the binding of RNA polymerase to the promoter
region, resulting in a large amount of gene expression (Fig. 4-5). Conversely, the
silencer suppresses gene expression.
Enhancers and silencers are different from promoters in that they function even if
they are located far upstream of the gene (sometimes dozens of kbp away), and
in some cases if they are inside or downstream of the gene. Promoters do not
exist inside or downstream of the gene because they represent points where RNA
polymerase binds, thereby initiating transcription. Another difference is that
enhancers and silencers can still function in the same way even if their sequences
are reversed. With promoters, the binding direction of RNA polymerase is
determined by the direction of the promoter sequence, based on which the
direction of enzyme movement and the selection of the template strand are
determined; if the sequence is reversed, the enzyme therefore proceeds in the
opposite direction, preventing the promoter from functioning.
It is common for single genes to contain multiple types of cis-element (such as
those described above) that regulate gene expression in accordance with various
intra- and extracellular signals. In eukaryotes, regions that regulate gene
expression are therefore very long, often exceeding 10 kbp.
Figure 4-4 Init iation of transcription from a eukaryotic promoter
Figure 4-5 Transcriptional activation by an enhancer
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The Possibility of Many Non-coding RNA Molecules Being miRNA Molecules
It has become increasingly clear that the nucleus of eukaryotes contains
more RNA types than first thought, many of which are non-coding RNA
molecules transcribed from DNA regions that are wider than initial estimations
(see the Column on p. 54 in Chapter 3). Many of these are relatively small
RNA molecules, and many of them form double-stranded structures based on
their functions, it is feasible to suggest that they may be miRNA. Since
miRNA plays a number of basic and important roles (including gene
expression regulation at chromosome and mRNA level), if the large amounts
of RNA present in cells turns out to be miRNA, our perception of expression
regulation in eukaryotic cellular genes will dramatically change. Research in
this area is progressing rapidly.
Regulation by Chromatin Remodeling
Eukaryotic DNA exists as nucleosomes structure in which DNA firmly binds to
histones (basic proteins) (Fig. 4-6). These nucleosomes then form a chromatin
fiber. When histones and DNA are tightly connected, it is difficult for RNA
polymerase to bind to the DNA and synthesize RNA. One of the roles of
enhancers is to loosen the connection between histones and DNA (and, in some
cases, deconstruct the nucleosomes) to promote RNA synthesis by RNA
Column
Figure 4-6 Construction of chromosomes from DNA
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polymerase. This phenomenon is called chromatin remodeling because it
changes the nucleosome structure.
Regulation by chromatin remodeling is a complex reaction in which large numbers
of enzymes and proteins are involved. To give a simplified explanation, a
transcriptional activation protein binds to a particular enhancer, which induces
histone acetyltransferase to also bind to the enhancer, thereby acetylating the
amino group of histones. This lowers the basicity of the histones, thus weakening
their connection with DNA. With this as a turning point, dissociation between
histones and DNA proceeds to neighboring regions; this soon exposes the
promoter, thereby facilitating the binding of the RNA polymerase complex to it
(Fig. 4-7). Conversely, when expression is suppressed, histone deacetylase
detaches the acetyl group to restore the nucleosome structure.
Column Figure 4-7 Loosening of the nucleosome structure by a transcription factors
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To investigate gene functions in traditional Mendelian genetics, the inheritance
patterns of the phenotypes (or traits) of an organism are first observed, and
then the characteristics of the genes that control the phenotypes in question
are analyzed. Simply put, analysis starts from phenotypes and moves toward
genes, with gene cloning as one of the goals.
On the other hand, while genes can now be easily cloned thanks to the
completion of the Human Genome Project and other scientific advances, the
nature of phenotypes brought about by the creation of cloned genes remains
largely unknown. Analysis that starts from the genes obtained and moves
toward phenotypes (gene functions) is called reverse genetics.
Often in reverse genetics, a knockout cell is made using one of the genes
obtained. An animal (such as a knockout mouse) is then cloned from this cell,
and the phenotypes of the animal are then analyzed (see the Column on p.
246 in Chapter 12). Despite the low success rate of this method, breakthroughs
have been made using the technique in areas where gene functions were
previously difficult to investigate, such as the functions of genes involved in the
developmental process and those involved in the higher functions of the brain.
Cloned animals and plants in which foreign genes have been artificially
introduced are called transgenic animals and plants. They are used to
analyze genes whose functions are unknown, and are also widely used in
applied research to create livestock that produces particular proteins.
Chromatin Structure and Gene Expression Regulation
In the DNA of non-expressed genes associated with differentiation functions,
cytosines – a type of nucleobase – are highly methylated. At sites with a two-base
sequence of 5’-CG-3’ in particular, over 70% of cytosines are methylated. If a large
number of methylated cytosines exist in the DNA that constitutes a nucleosome, the
protein complex that recognizes them binds to the DNA, and the histone
methyltransferase contained in the complex methylates histones. A protein then
binds to the methylated histones, tightly packing the chromatins at the site (Fig. 4-8).
This structure is called a constitutive heterochromatin (see the Column on p.81).
Conversely, methylation occurs to a lesser extent in genes that are expressed.
Column Genetics and Reverse Genetics
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When cells grow, the cytosines in the newly created DNA strand (i.e., the
daughter strand) are not methylated. However, if the cytosines at some sites in the
template strand (i.e., the parent strand) are methylated (the sequence is 5’-CG-3’
in both strands), an enzyme methylates the cytosines in the daughter strand at
locations opposite the methylated parts of the template, thus maintaining the
methylated state of both the parent and daughter strands. In this way, non-
expressed genes in heterochromatin domains are inherited through cell division
to progeny cells in unchanged form. In such cases, methylation information is
passed on to progeny cells in the same way as changes in DNA sequences
(genetic changes, or mutations), but no changes in sequence actually occur. The
phenomenon is known as epigenetic change, and this type of gene expression
regulation is called epigenetic regulation (Fig. 4-8).
Figure 4-8 Schematic diagram of the epigenetic regulation mechanism
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Under a microscope, it can be seen that a nucleus consists of heterochromatin
and euchromatin. The former is stained dark when basic dye is applied, while
the latter exhibits light staining. In heterochromatin, chromatin fibers are bound
with proteins, thereby tightly packing chromatins in which non-expressed genes
are concentrated. Euchromatin is a loosely packed form of chromatin in which
genes that can be expressed are concentrated. Heterochromatin is believed to
consist of constitutive heterochromatin and facultative heterochromatin.
Throughout the life of the cell, constitutive heterochromatin domains form
heterochromatin, in which the expression of genes is suppressed. One of the
two X chromosomes in women is packaged in constitutive heterochromatin. An
often-quoted fact is that the serum albumin gene is not expressed in any cell
except hepatocytes, probably because it dwells within constitutive
heterochromatin. Facultative heterochromatin is a type of heterochromatin that
moves between heterochromatin and euchromatin states.
DNA methylation is closely associated with heterochromatin formation, and
the genes in highly methylated DNA sites are not expressed. The DNA in the
cells between the germ-cell and early development stages is hypomethylated,
meaning that all genes during this period can be expressed. It can also be
said that all such cells have totipotency – the ability to develop into all cell
types. As somatic cells become more differentiated during the developmental
process, DNA methylation gradually proceeds, thus limiting the paths of
differentiation for those cells (although the regions methylated differ by cell
type). Subsequently, most of the genes associated with differentiation functions
(except for some specific genes) become highly methylated, meaning that
they will never need to be expressed. Although the mechanism of particular
DNA regions becoming methylated during the developmental process is not
yet clear, it is understood that this developmental process is where DNA
methylation proceeds. One of the reasons for the low success rate of animal
cloning from somatic cells may be the lack of methods to efficiently transform
hypermethylated DNA to a hypomethylated state (i.e., initialization).
Column Heterochromatin and Euchromatin
Column DNA Methylation, Development and Somatic Cell Cloned Animals
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The aim of the Human Genome Project was to determine the entire DNA
sequence of humans. In addition to this, the complete sequences of over 20
species of organism have so far been determined or almost determined. The
term genome refers to the entire collection of DNA in one cell; although only
a small portion of the genome functions as genes, in functional terms the
word refers to the entire collection of genes in one cell. Using the success of
the Human Genome Project as a springboard, several projects have been
implemented in which the functions of organisms are comprehensively
investigated (rather than concentrating on individual species). As an
example, one area of investigation focuses on transcriptomes – the set of all
RNA molecules transcribed (transcripts) – in terms of the types and amounts
of mRNA synthesized in particular tissues or cells. These should differ by
organ, tissue and cell in the same species, and should also naturally change
in line with alterations in physiological function or when the organism is
diseased. It is expected that comprehensive investigation of these areas will
enable the identification of changes in mRNA types and amounts in diseased
conditions as well as in normal ones. Likewise, comprehensive analyses are
under way in areas such as proteomes (the entire complement of proteins
expressed), interactomes (the whole set of protein associations and
interactions), metabolomes (the complete set of all metabolites) and
epigenomes (overall epigenetic changes, including DNA methylation).
Some joke that we are now in the era of the “ome.”
Column Genomes, Transcriptomes and Proteomes
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• Genes are not always active; their expression is regulated as appropriate.
• Genes are roughly classified as housekeeping genes (essential for the
survival and proliferation of cells) and those involved in differentiation
(essential for the functioning of multicellular organisms).
• Housekeeping genes are present in both prokaryotes and eukaryotic
multicellular organisms, whereas genes involved in differentiation are
unique to eukaryotic multicellular organisms.
• The housekeeping type consists of constitutive genes, which are
continuously expressed, and regulated expression genes.
• Regulated expression involves transcription factors (proteins) that recognize
and bind to the sequence of the promoter region. Through this binding,
transcription is regulated both positively and negatively.
• Gene expression in prokaryotes is often caused by the presence/absence
of mRNA synthesis, i.e., by transcriptional regulation.
• In eukaryotes, posttranscriptional regulation occurs in addition to
transcriptional regulation. This includes the modification of mRNA and the
transportation of mRNA from the nucleus to the cytoplasm.
• In addition to promoters, eukaryotes have gene expression regulation
regions known as enhancers and silencers in their DNA. Gene expression is
regulated when particular proteins (transcriptional regulator) bind to them.
• In eukaryotes, DNA intertwines with histones (basic proteins) to form
nucleosomes, which connect with other proteins to form chromatin.
• Expression regulation by enhancers or silencers is sometimes accompanied
by changes in chromatin structure (chromatin remodeling).
• Genes that can be expressed are located in regions where chromatin is
loosely packed (i.e., areas of euchromatin), whereas genes that are never
expressed are often concentrated in regions where chromatin is tightly
packed (i.e., areas of heterochromatin).
Summary Chapter 4
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[1]
The expression of the β-galactosidase gene in E. coli is
regulated both positively and negatively. Briefly explain
these two mechanisms.
[2]
In eukaryotic multicellular organisms, each differentiated cell
type has a unique gene expression pattern – a characteristic
that is preserved even after cell division. In hepatocytes, for
example, genes involved in differentiation unique to cells are
expressed, and the expression pattern is different from that
in osteocytes. Although it may appear that these cells have
different genes and pass them on to their progeny cells, the
genes are in fact the same, but in many cases may have
undergone changes.
1) Provide the name of the gene-level change behind these
phenomena.
2) Describe the mechanism that causes such changes.
[3]
Organisms are considered to adapt to their habitat by
effectively regulating gene expression while responding to
environmental conditions and external substances. Using an
example, describe genes that are regulated in response to
environmental factors.
[4]
In eukaryotes, a mRNA molecules is normally transcribed
from single gene (i.e., monocistronic mRNA), whereas in
prokaryotes, it is often transcribed from multiple related
genes in series (i.e., polycistronic mRNA). Describe the
advantages and disadvantages of these two mechanisms in