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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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Chapter 4 Regulation of Gene Expression - Life Science

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Page 1: Chapter 4 Regulation of Gene Expression - Life Science

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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

the regulation of gene expression.

Problems

(Answers on p.252)