Seyed Abolfazl Motahari

Microarray DataAnalysis

Applications

Measurements

• Genotypes: Single nucleotide polymorphism (SNP) microarrays.

• DNA methylation.

• DNA copy numbers: Array comparative genomic hybridization (aCGH).

• Tag quantitation: Genetic Screening.

• Transcript (mRNA) levels: mRNA-Chip.

• Alternative splicing: Exon and exon-exon splice junction microarrays.

• mRNA degradation rate

• RNA capture

DNA RNA

Gene-Chip

Genotypes:  AA  AC  CC

Gene-Chip: Biological Questions

Detection of sequence variation Genetic typing Detection of somatic mutations (e.g. in oncogenes) Direct sequencing

RNA-Chip

● Gene Expression: – The process by which the information encoded in a gene is converted into an

observable phenotype (most commonly production of a protein). – The degree to which a gene is active in a certain tissue of the body, measured

by the amount of mRNA in the tissue.

55 genes are over-expressed and 480 under-expressed in cells of a prostate cancer that has a very high likelihood of spreading—but not in a prostate cancer that will not spread.

Example:

RNA-Chip

● Functional Genomics: – Systematic analysis of gene activity in healthy and diseased tissues. – Obtaining an overall picture of genome functions, including the expression

profiles at the mRNA level and the protein level.

● Functional Genome Analysis: – used to understand the functions of genes and proteins in an organism. This is

typically known as genome annotation. – used in integrative biology and systems biology studies aiming to understand

health and disease states (e.g. cancer, obesity, …etc) – Used as an important step in the search for new target molecules in the drug

discovery process. (which genes, proteins to target and how)

Biological Organization

Lewis:  Human  Genetics:  Concepts  Applications

Lewis: Human Genetics: Concepts and Applications, Ninth Edition

I. Introduction 1. Overview of Genetics8 © The McGraw−Hill Companies, 2010

6 Part 1 Introduction

disorders are so rare that they do not even have a name. The open-ing essay to chapter 4 describes a little girl in this situation.

The Bigger Picture: From Populations to Evolution Above the family level of genetic organization is the popula-tion. In a strict biological sense, a population is a group of inter-breeding individuals. In a genetic sense, a population is a large collection of alleles, distinguished by their frequencies. People from a Swedish population, for example, would have a greater frequency of alleles that specify light hair and skin than people from a population in Ethiopia, who tend to have dark hair and skin. The fact that groups of people look different and may suffer from different health problems reflects the frequencies of their distinctive sets of alleles. All the alleles in a population consti-tute the gene pool. (An individual does not have a gene pool.)

Population genetics is applied in health care, foren-sics, and other fields. It is also the basis of evolution, which is defined as changing allele frequencies in populations. These small-scale genetic changes foster the more obvious species distinctions we most often associate with evolution.

Comparing DNA sequences for individual genes, or the amino acid sequences of the proteins that the genes encode, can reveal how closely related different types of organisms are ( figure 1.4 ). The underlying assumption is that the more similar the sequences are, the more recently two species diverged from a shared ances-tor. This is a more plausible explanation than two species having evolved similar or identical gene sequences by chance.

begins with transmission genetics, when an interesting family trait or illness comes to a researcher’s attention. Charts called pedigrees represent the members of a family and indicate which individuals have particular inherited traits. Chapter 4 includes many pedigrees.

Sometimes understanding a rare condition inherited as a single-gene trait leads to treatments for the greater number of peo-ple with similar disorders that are not inherited. This is the case for the statin drugs widely used to lower cholesterol. Still, despite the availability of the human genome sequence, some single-gene

Table 1.2 Tissue Types

Tissue Function/Location/Description

Connective tissues

A variety of cell types and materials around them that protect, support, bind to cells and fill spaces throughout the body; include cartilage, bone, blood, and fat

Epithelium Tight cell layers that form linings that protect, secrete, absorb, and excrete

Muscle Cells that contract, providing movement

Nervous Neurons transmit information as electrochemical impulses that coordinate movement and sense and respond to environmental stimuli; neuroglia are cells that support and nourish neurons

Atom

Molecule

Macromolecule

Organelle

CellCell

Tissue

Organ

Organism

Organ system

Figure 1.3 Levels of biological organization.

Lewis: Human Genetics: Concepts and Applications, Ninth Edition

I. Introduction 1. Overview of Genetics8 © The McGraw−Hill Companies, 2010

6 Part 1 Introduction

disorders are so rare that they do not even have a name. The open-ing essay to chapter 4 describes a little girl in this situation.

The Bigger Picture: From Populations to Evolution Above the family level of genetic organization is the popula-tion. In a strict biological sense, a population is a group of inter-breeding individuals. In a genetic sense, a population is a large collection of alleles, distinguished by their frequencies. People from a Swedish population, for example, would have a greater frequency of alleles that specify light hair and skin than people from a population in Ethiopia, who tend to have dark hair and skin. The fact that groups of people look different and may suffer from different health problems reflects the frequencies of their distinctive sets of alleles. All the alleles in a population consti-tute the gene pool. (An individual does not have a gene pool.)

Population genetics is applied in health care, foren-sics, and other fields. It is also the basis of evolution, which is defined as changing allele frequencies in populations. These small-scale genetic changes foster the more obvious species distinctions we most often associate with evolution.

Comparing DNA sequences for individual genes, or the amino acid sequences of the proteins that the genes encode, can reveal how closely related different types of organisms are ( figure 1.4 ). The underlying assumption is that the more similar the sequences are, the more recently two species diverged from a shared ances-tor. This is a more plausible explanation than two species having evolved similar or identical gene sequences by chance.

begins with transmission genetics, when an interesting family trait or illness comes to a researcher’s attention. Charts called pedigrees represent the members of a family and indicate which individuals have particular inherited traits. Chapter 4 includes many pedigrees.

Sometimes understanding a rare condition inherited as a single-gene trait leads to treatments for the greater number of peo-ple with similar disorders that are not inherited. This is the case for the statin drugs widely used to lower cholesterol. Still, despite the availability of the human genome sequence, some single-gene

Table 1.2 Tissue Types

Tissue Function/Location/Description

Connective tissues

A variety of cell types and materials around them that protect, support, bind to cells and fill spaces throughout the body; include cartilage, bone, blood, and fat

Epithelium Tight cell layers that form linings that protect, secrete, absorb, and excrete

Muscle Cells that contract, providing movement

Nervous Neurons transmit information as electrochemical impulses that coordinate movement and sense and respond to environmental stimuli; neuroglia are cells that support and nourish neurons

Atom

Molecule

Macromolecule

Organelle

CellCell

Tissue

Organ

Organism

Organ system

Figure 1.3 Levels of biological organization.

Lewis: Human Genetics: Concepts and Applications, Ninth Edition

I. Introduction 1. Overview of Genetics8 © The McGraw−Hill Companies, 2010

6 Part 1 Introduction

disorders are so rare that they do not even have a name. The open-ing essay to chapter 4 describes a little girl in this situation.

The Bigger Picture: From Populations to Evolution Above the family level of genetic organization is the popula-tion. In a strict biological sense, a population is a group of inter-breeding individuals. In a genetic sense, a population is a large collection of alleles, distinguished by their frequencies. People from a Swedish population, for example, would have a greater frequency of alleles that specify light hair and skin than people from a population in Ethiopia, who tend to have dark hair and skin. The fact that groups of people look different and may suffer from different health problems reflects the frequencies of their distinctive sets of alleles. All the alleles in a population consti-tute the gene pool. (An individual does not have a gene pool.)

Population genetics is applied in health care, foren-sics, and other fields. It is also the basis of evolution, which is defined as changing allele frequencies in populations. These small-scale genetic changes foster the more obvious species distinctions we most often associate with evolution.

Comparing DNA sequences for individual genes, or the amino acid sequences of the proteins that the genes encode, can reveal how closely related different types of organisms are ( figure 1.4 ). The underlying assumption is that the more similar the sequences are, the more recently two species diverged from a shared ances-tor. This is a more plausible explanation than two species having evolved similar or identical gene sequences by chance.

begins with transmission genetics, when an interesting family trait or illness comes to a researcher’s attention. Charts called pedigrees represent the members of a family and indicate which individuals have particular inherited traits. Chapter 4 includes many pedigrees.

Sometimes understanding a rare condition inherited as a single-gene trait leads to treatments for the greater number of peo-ple with similar disorders that are not inherited. This is the case for the statin drugs widely used to lower cholesterol. Still, despite the availability of the human genome sequence, some single-gene

Table 1.2 Tissue Types

Tissue Function/Location/Description

Connective tissues

A variety of cell types and materials around them that protect, support, bind to cells and fill spaces throughout the body; include cartilage, bone, blood, and fat

Epithelium Tight cell layers that form linings that protect, secrete, absorb, and excrete

Muscle Cells that contract, providing movement

Nervous Neurons transmit information as electrochemical impulses that coordinate movement and sense and respond to environmental stimuli; neuroglia are cells that support and nourish neurons

Atom

Molecule

Macromolecule

Organelle

CellCell

Tissue

Organ

Organism

Organ system

Figure 1.3 Levels of biological organization.

Lewis: Human Genetics: Concepts and Applications, Ninth Edition

I. Introduction 1. Overview of Genetics8 © The McGraw−Hill Companies, 2010

6 Part 1 Introduction

disorders are so rare that they do not even have a name. The open-ing essay to chapter 4 describes a little girl in this situation.

The Bigger Picture: From Populations to Evolution Above the family level of genetic organization is the popula-tion. In a strict biological sense, a population is a group of inter-breeding individuals. In a genetic sense, a population is a large collection of alleles, distinguished by their frequencies. People from a Swedish population, for example, would have a greater frequency of alleles that specify light hair and skin than people from a population in Ethiopia, who tend to have dark hair and skin. The fact that groups of people look different and may suffer from different health problems reflects the frequencies of their distinctive sets of alleles. All the alleles in a population consti-tute the gene pool. (An individual does not have a gene pool.)

Population genetics is applied in health care, foren-sics, and other fields. It is also the basis of evolution, which is defined as changing allele frequencies in populations. These small-scale genetic changes foster the more obvious species distinctions we most often associate with evolution.

Comparing DNA sequences for individual genes, or the amino acid sequences of the proteins that the genes encode, can reveal how closely related different types of organisms are ( figure 1.4 ). The underlying assumption is that the more similar the sequences are, the more recently two species diverged from a shared ances-tor. This is a more plausible explanation than two species having evolved similar or identical gene sequences by chance.

begins with transmission genetics, when an interesting family trait or illness comes to a researcher’s attention. Charts called pedigrees represent the members of a family and indicate which individuals have particular inherited traits. Chapter 4 includes many pedigrees.

Sometimes understanding a rare condition inherited as a single-gene trait leads to treatments for the greater number of peo-ple with similar disorders that are not inherited. This is the case for the statin drugs widely used to lower cholesterol. Still, despite the availability of the human genome sequence, some single-gene

Table 1.2 Tissue Types

Tissue Function/Location/Description

Connective tissues

A variety of cell types and materials around them that protect, support, bind to cells and fill spaces throughout the body; include cartilage, bone, blood, and fat

Epithelium Tight cell layers that form linings that protect, secrete, absorb, and excrete

Muscle Cells that contract, providing movement

Nervous Neurons transmit information as electrochemical impulses that coordinate movement and sense and respond to environmental stimuli; neuroglia are cells that support and nourish neurons

Atom

Molecule

Macromolecule

Organelle

CellCell

Tissue

Organ

Organism

Organ system

Figure 1.3 Levels of biological organization.

Cell Differentiation

Lewis: Human Genetics: Concepts and Applications, Ninth Edition

I. Introduction 2. Cells40 © The McGraw−Hill Companies, 2010

38 Part 1 Introduction

Sperm

Egg

Fertilized egg

Stem cell

Stem cell

Progenitor cell

Progenitorcell

Progenitorcell

Progenitorcell

Progenitorcell

Progenitorcells

Blood cells and platelets

Connective tissue cell(fibroblast)

Bone cell

Progenitorcell

Progenitorcell

Astrocyte

Neuron

Skin cell

Sebaceousgland cell

one or more steps

produces another stem cell(self-renewal)

Progenitorcell

Progenitorcells

Figure 2.23 Pathways to cell specialization. All cells in the human body descend from stem cells, through the processes of mitosis and differentiation. The differentiated cells on the lower left are all connective tissues (blood, connective tissue, and bone), but the blood cells are more closely related to each other than they are to the other two cell types. On the upper right, the skin and sebaceous gland cells share a recent progenitor, and both share a more distant progenitor with neurons and supportive astrocytes. Imagine how complex the illustration would be if it embraced all 260-plus types of cells in a human body!

a chemistry major, she would not need to start from scratch because many of the same courses apply to both majors. So it is for stem cells. Taking a skin cell from a man with heart disease and turning it into a healthy heart muscle cell might require

taking that initial cell back to an ES or iPS state, because these cells come from very different lineages. But turning an endo-crine cell of the pancreas into a digestive cell of the pancreas requires fewer steps backwards.

Cell Differentiation

Lewis: Human Genetics: Concepts and Applications, Ninth Edition

I. Introduction 3. Meiosis and Development

58 © The McGraw−Hill Companies, 2010

56 Part 1 Introduction

By 10 weeks, the placenta is fully formed. The placenta is an organ that links woman and fetus for the rest of the pregnancy. The placenta secretes hormones that maintain preg-nancy and alter the woman’s metabo-lism to send nutrients to the fetus.

Other structures nurture the developing embryo. The yolk sac manufactures blood cells, as does the allantois, a membrane surrounding the embryo that gives rise to the umbilical blood vessels. The umbilical cord forms around these vessels and attaches to the center of the placenta. Toward the end of the embryonic period, the yolk sac shrinks, and the amniotic sac swells with fluid that cushions the embryo and maintains a constant temperature and pressure. The amniotic fluid con-tains fetal urine and cells.

Two of the supportive struc-tures that develop during pregnancy provide the material for prenatal tests (see figure 13.5), discussed in chap-ter 13. Chorionic villus sampling examines chromosomes from cells snipped off the chorionic villi at 10 weeks. Because the villi cells and the embryo’s cells come from the same fertilized ovum, an abnormal chromo-some in villi cells should also be in the embryo. In amniocentesis, a sample of amniotic fluid is taken and fetal cells in it are examined for biochemical, genetic, and chromosomal anomalies.

The umbilical cord is another prenatal structure that has medical applications. In addition to the cord blood banks mentioned in Bioethics: Choices for the Future in chapter 2, the cells of the cord itself are valu-

able. When cultured in the same “cocktails” used for embryonic stem cells, cord cells can dif-ferentiate as cells from any of the three primary germ layers, including bone, fat, nerve, carti-lage, and muscle cells. Stem cells from the cord are used to treat a respiratory disease of newborns that scars and inflames the lungs. The stem cells become two types of needed lung cells: the type that secretes surfactant, which is the chemical that inflates the micro-scopic air sacs, and the type that

Amnion

Amniotic fluid

Heart

Digestive tract

Skin

Spinal cord

Chorion

Tail end

Body stalk with umbilicalblood vessels

Trophoblast

Brain

Yolk sac

Ectoderm

Epidermis of skin and epidermalderivatives: hair, nails, glandsof the skin; linings of cavities

Nervous tissue; sensory organsLens of eye; tooth enamelPituitary glandAdrenal medulla

Mesoderm

MuscleConnective tissue:

cartilage, bone, bloodDermis of skin; dentin of teethEpithelium of blood vessels,

lymphatic vessels, cavitiesInternal reproductive organsKidneys and uretersAdrenal cortex

Endoderm

Epithelium of pharynx, auditory canal, tonsils, thyroid, parathyroid, thymus, larynx, trachea, lungs, digestive tract, urinary bladder and urethra,vagina

Liver and pancreas

Figure 3.15 The primordial embryo. When the three primary germ layers of the embryo form at gastrulation, many cells become “fated” to follow a specific developmental pathway. Each layer retains stem cells as the organism develops. Under certain conditions, these cells may produce daughter cells that can specialize as many cell types.

Stage Time Period Principal Events

Fertilized ovum

12–24 hours following ovulation

Oocyte fertilized; zygote has 23 pairs of chromosomes and is genetically distinct

Cleavage 30 hours to third day Mitosis increases cell number

Morula Third to fourth day Solid ball of cells

Blastocyst Fifth day through second week

Hollowed ball forms trophoblast (outside) and inner cell mass, which implants and flattens to form embryonic disc

Gastrula End of second week Primary germ layers form

Table 3.2 Stages and Events of Early Human Prenatal Development

When the three primary germ layers of the embryo form at gastrulation, many cells become “fated” to follow a specific developmental pathway. Each layer retains stem cells as the organism develops. Under certain conditions, these cells may produce daughter cells that can specialize as many cell types.

Gene Expression Through Time and TissueLewis: Human Genetics: Concepts and Applications, Ninth Edition

III. DNA and Chromosomes 11. Gene Expression and Epigenetics

205© The McGraw−Hill Companies, 2010

Chapter 11 Gene Expression and Epigenetics 203

11.1 Gene Expression Through Time and Tissue A genome is like an orchestra. Just as not all of the instruments play with the same intensity at every moment, not all genes are expressed continually at the same levels. Before the field of genomics began in the 1990s, the study of genetics proceeded one gene at a time, like hearing the separate contributions of a violin, a viola, and a flute. Many genetic investigations today, in contrast, track the crescendos of gene activity that parallel events in an organism’s life. This new view has introduced the element of time to genetic analysis. Unlike the gene maps of old, which ordered genes on chromosomes, new types of maps reveal the timing of gene expression in unfolding programs of development and response to the environment.

The discoveries of the 1950s and 1960s on DNA struc-ture and function answered some questions about the control of gene expression while raising many more. How does a bone cell “know” to transcribe the genes that control the synthesis of collagen and not to transcribe genes that specify muscle pro-teins? What causes the proportions of blood cell types to shift into leukemia? How do chemical groups “know” to shield DNA from transcription in one circumstance, yet expose it in others?

Changes to the chemical groups that associate with DNA profoundly affect which parts of the genome are accessible to transcription factors and under which conditions. Such changes to the molecules that bind to DNA that are transmitted to daughter cells when the cell divides are termed epigenetic —literally, “outside the gene.”

Specific classes of proteins and RNA molecules carry out epigenetic changes, and much of the genome encodes these modi-fiers of gene expression. Although research is currently focusing on identifying epigenetic changes in different cell types under dif-ferent conditions, the idea of modifying gene expression is not new. British embryologist C. H. Waddington wrote in 1939 of “the causal interactions between genes and their prod-ucts which bring the phenotype into being.” Epigenetic changes do not alter the DNA base sequence, although they are passed from one cell generation to the next.

This chapter extends the discussion of DNA structure and function from the encoding of informa-tion to how that information is accessed. We begin with three examples at the molecular, tissue, and organ levels: (1) hemoglobin switching during development; (2) the composition of blood plasma, and; (3) special-ization of the two major parts of the pancreas.

Globin Chain Switching The globin proteins that transport oxygen in the blood vividly illustrate control of gene expression. The mol-ecule’s changing composition through development was discovered half a century ago.

A hemoglobin molecule in the blood of an adult has four polypeptide chains, each wound into a globu-lar conformation ( figure 11.1 ). Two of the chains are

146 amino acids long and are called “beta” ( β ). The other two chains are 141 amino acids long and are termed “alpha” ( α ). The genes for beta subunits are clustered on chromosome 11, and the alpha genes are grouped on chromosome 16.

The subunits of the hemoglobin molecule are replaced as the oxygen concentration in the body changes, which in turn depends upon whether oxygen arrives to an embryo or fetus through the placenta or to a newborn’s lungs from breathing. The chemical basis for this “globin chain switching” is that different polypeptide subunits attract oxygen molecules to dif-ferent degrees. Parts of the globin gene clusters oversee the changes in the molecule’s composition and assembly.

The subunit makeup of the hemoglobin molecule differs in the embryo, fetus, and adult ( figure 11.2 ). In the embryo,

Beta chain

Alpha chain

Beta chain

Alpha chain

Heme group

Heme group

Figure 11.1 The structure of hemoglobin. A hemoglobin molecule is made up of two globular protein chains from the beta (β) globin group and two from the alpha (α) globin group. Each globin surrounds an iron-containing chemical group called a heme.

Figure 11.2 Globin chain switching. The subunit composition of human hemoglobin changes as the concentration of oxygen in the environment changes. With the switch from the placenta to the newborn’s lungs to obtain oxygen, beta (β) globin begins to replace gamma (γ) globin.

β

γ

α α

δζ

ε

ζ ζεε

α αγγ

α αββ

Birth

Weeks after birth

Per

cent

of t

otal

glo

bin

synt

hesi

s

Weeks after fertilization

Embryonic Fetal Adult

50

40

30

20

10

0 6 12 18 24 30 36 0 484236302418126

Lewis: Human Genetics: Concepts and Applications, Ninth Edition

III. DNA and Chromosomes 11. Gene Expression and Epigenetics

205© The McGraw−Hill Companies, 2010

Chapter 11 Gene Expression and Epigenetics 203

11.1 Gene Expression Through Time and Tissue A genome is like an orchestra. Just as not all of the instruments play with the same intensity at every moment, not all genes are expressed continually at the same levels. Before the field of genomics began in the 1990s, the study of genetics proceeded one gene at a time, like hearing the separate contributions of a violin, a viola, and a flute. Many genetic investigations today, in contrast, track the crescendos of gene activity that parallel events in an organism’s life. This new view has introduced the element of time to genetic analysis. Unlike the gene maps of old, which ordered genes on chromosomes, new types of maps reveal the timing of gene expression in unfolding programs of development and response to the environment.

The discoveries of the 1950s and 1960s on DNA struc-ture and function answered some questions about the control of gene expression while raising many more. How does a bone cell “know” to transcribe the genes that control the synthesis of collagen and not to transcribe genes that specify muscle pro-teins? What causes the proportions of blood cell types to shift into leukemia? How do chemical groups “know” to shield DNA from transcription in one circumstance, yet expose it in others?

Changes to the chemical groups that associate with DNA profoundly affect which parts of the genome are accessible to transcription factors and under which conditions. Such changes to the molecules that bind to DNA that are transmitted to daughter cells when the cell divides are termed epigenetic —literally, “outside the gene.”

Specific classes of proteins and RNA molecules carry out epigenetic changes, and much of the genome encodes these modi-fiers of gene expression. Although research is currently focusing on identifying epigenetic changes in different cell types under dif-ferent conditions, the idea of modifying gene expression is not new. British embryologist C. H. Waddington wrote in 1939 of “the causal interactions between genes and their prod-ucts which bring the phenotype into being.” Epigenetic changes do not alter the DNA base sequence, although they are passed from one cell generation to the next.

This chapter extends the discussion of DNA structure and function from the encoding of informa-tion to how that information is accessed. We begin with three examples at the molecular, tissue, and organ levels: (1) hemoglobin switching during development; (2) the composition of blood plasma, and; (3) special-ization of the two major parts of the pancreas.

Globin Chain Switching The globin proteins that transport oxygen in the blood vividly illustrate control of gene expression. The mol-ecule’s changing composition through development was discovered half a century ago.

A hemoglobin molecule in the blood of an adult has four polypeptide chains, each wound into a globu-lar conformation ( figure 11.1 ). Two of the chains are

146 amino acids long and are called “beta” ( β ). The other two chains are 141 amino acids long and are termed “alpha” ( α ). The genes for beta subunits are clustered on chromosome 11, and the alpha genes are grouped on chromosome 16.

The subunits of the hemoglobin molecule are replaced as the oxygen concentration in the body changes, which in turn depends upon whether oxygen arrives to an embryo or fetus through the placenta or to a newborn’s lungs from breathing. The chemical basis for this “globin chain switching” is that different polypeptide subunits attract oxygen molecules to dif-ferent degrees. Parts of the globin gene clusters oversee the changes in the molecule’s composition and assembly.

The subunit makeup of the hemoglobin molecule differs in the embryo, fetus, and adult ( figure 11.2 ). In the embryo,

Beta chain

Alpha chain

Beta chain

Alpha chain

Heme group

Heme group

Figure 11.1 The structure of hemoglobin. A hemoglobin molecule is made up of two globular protein chains from the beta (β) globin group and two from the alpha (α) globin group. Each globin surrounds an iron-containing chemical group called a heme.

Figure 11.2 Globin chain switching. The subunit composition of human hemoglobin changes as the concentration of oxygen in the environment changes. With the switch from the placenta to the newborn’s lungs to obtain oxygen, beta (β) globin begins to replace gamma (γ) globin.

β

γ

α α

δζ

ε

ζ ζεε

α αγγ

α αββ

Birth

Weeks after birth

Per

cent

of t

otal

glo

bin

synt

hesi

s

Weeks after fertilization

Embryonic Fetal Adult

50

40

30

20

10

0 6 12 18 24 30 36 0 484236302418126

Globin  Chain  Switching

Questions:  1-­‐  Mutations  in  alpha  2-­‐  Mutations  in  beta

Gene Expression Through Time and Tissue

Lewis: Human Genetics: Concepts and Applications, Ninth Edition

III. DNA and Chromosomes 11. Gene Expression and Epigenetics

206 © The McGraw−Hill Companies, 2010

204 Part 3 DNA and Chromosomes

see which combinations of growth factors, hormones, and other biochemicals must be added to steer development toward a par-ticular cell type.

Consider the pancreas. It is a dual gland, with two types of cell clusters. The exocrine part releases digestive enzymes into ducts, whereas the endocrine part secretes polypeptide hor-mones that control nutrient use directly into the bloodstream. The endocrine cell clusters are called pancreatic islets.

The complexity of the pancreas unfolds in the embryo, when ducts form. Within duct walls reside rare stem cells and progenitor cells (see figure 2.22). Recall that a stem cell is an unspecialized cell that divides to yield another stem cell (self-renewal), and a progenitor cell that is partially spe-cialized. When a transcription factor called pdx-1 is acti-vated, it in turn controls expression of other genes in a way that stimulates some of the progenitor cells to divide. Some of the progenitor cells give rise to daughter cells that follow an exocrine pathway; they are destined to produce digestiveenzymes (figure 11.3). Other progenitor cells respond to dif-ferent signals and divide to yield daughters that follow the endocrine pathway. The most familiar pancreatic hormone is

as the placenta forms, hemoglobin consists first of two epsilon (ε) chains, which are in the beta globin group, and two zeta ( ζ ) chains, which are in the alpha globin group. About 4 percent of the hemoglobin in the embryo includes beta chains. This percentagegradually increases.

As the embryo develops into a fetus, the epsilon and zeta chains decrease in number, as gamma (γ ) and alpha chains accu-mulate. Hemoglobin consisting of two gamma and two alpha chains is called fetal hemoglobin. The gamma globin subunits bind very strongly to oxygen released from maternal red blood cells into the placenta, so that fetal blood carries 20 to 30 percent more oxygen than an adult’s blood. As the fetus matures, beta chains gradually replace the gamma chains. At birth, however, the hemoglobin is not fully of the adult type—fetal hemoglobin (two gamma and two alpha chains) comprises from 50 to 85 percent of the blood. By four months of age, the proportion drops to 10 to 15 percent, and by four years, it is less than 1 percent.

Building Tissues and Organs The globin chains affect one type of molecule, hemoglobin. Changing gene expression and the resulting production of pro-teins can also be observed on a larger scale, such as the num-bers of different types and amounts of proteins in particular tissues. For example, blood plasma, the liquid portion of blood, contains about 40,000 different types of proteins. Ten types of proteins account for 90 percent of all the plasma protein molecules, and nearly half of those are one type, albumin. Many thou-sands of types of proteins make up the rest, and are present in very small amounts. If conditions change, such as a person developing an infection or allergic reaction, the protein pro-file of the plasma can change dra-matically. This ability of the tissue to adapt to a changing environment is possible because of changes in gene expression—that is, how much of each protein is made.

Blood is a structurally simple tissue that is easy to obtain and study. A solid gland or organ, con-structed from specialized cells and tissues, is much more complex. Its solid organization must be main-tained throughout a lifetime of growth, repair, and changing exter-nal conditions.

Stem cell biology is shedding light on how genes are turned on and off during the development of an organ or gland. Researchers iso-late individual stem cells and then

Figure 11.3 Building a pancreas. A single type of stem cell theoretically gives rise to an exocrine/endocrine progenitor cell that in turn divides to yield more restricted progenitor cells that give rise to both mature exocrine and endocrine cells. The endocrine progenitor cell in turn divides to give rise to cells that are specialized to produce particular hormones.

Stem cell Stem cell

Exocrine/endocrineprogenitor cell

Mature exocrinecell (acinar)

β cellsinsulin(70%)

α cellsglucagon(15%)

δ cellssomatostatin(10%)

F cellspancreaticpolypeptide(5%)

Endocrineprogenitorcell

Exocrineprogenitorcell

Pancreas

It is a dual gland, with two types of cell clusters. The exocrine part releases digestive enzymes into ducts, whereas the endocrine part secretes polypeptide hormones that control nutrient use directly into the bloodstream. The endocrine cell clusters are called pancreatic islets.

Gene Expression Through Time and Tissue

Lewis: Human Genetics: Concepts and Applications, Ninth Edition

III. DNA and Chromosomes 11. Gene Expression and Epigenetics

207© The McGraw−Hill Companies, 2010

Chapter 11 Gene Expression and Epigenetics 205

differentiation of this period. During the prenatal period, enzymes are less abundant, perhaps because the fetus receives some enzymes through the placenta. Immunoglob-ulins appear as a category after birth as the immune system begins to function.

Another way to look at the proteome is by specific functions, which has led to the creation of various “ome” words. Genes whose encoded proteins control lipid synthe-sis, for example, constitute the “lipidome,” and those that monitor carbohydrate production and use form the “glycome.” “Omics” designations are helpful in sorting out the thousands of proteins a human cell can manufacture. However, identify-ing proteins is only a first step. The next hurdle is to deter-mine how proteins with related functions interact—forming “interactomes.”

Gene expression profiles for different cell types under various conditions can provide valuable medical information and are the basis for many new tests that diagnose disease or monitor response to treatment. For example, 55 genes are over-expressed and 480 underexpressed in cells of a prostate cancer that has a very high likelihood of spreading—but not in a pros-tate cancer that will not spread. A test based on such findings assists physicians in deciding which patients can benefit most from further treatment.

insulin—its absence (or the inability of cells to recognize it) causes diabetes mellitus.

Researchers can observe the specialization of pancreas cells by taking individual progenitor cells from human pan-creas ducts or by deriving them from reprogrammed somatic cells (see figure 2.24). Then, by supplying specific growth factors at particular times, the progenitor cells give rise to clusters that look and function like pancreatic islets. When exposed to glucose, the cells secrete insulin! If pancreatic stem cells can be isolated and cultured, it might be possible to coax a person with diabetes to produce new and functional pancreatic beta cells.

Proteomics A more complete portrait of gene expression emerges through proteomics, which considers all proteins made in a cell, tissue, gland, organ, or entire body. Figure 11.4 depicts a global way of comparing the relative contributions of major categories of proteins from conception through birth and from conception through old age.

The differences in proteins produced at different times make sense. For example, transcription factors are more abundant before birth because of the extensive cell

Unknown

Immunoglobulins

Enzymes

Modulatorsof proteinfunctionReceptors

Transcriptionfactors

Intracellularmatrix

Extracellularmatrix

Transmembranetransporters

b. Distribution of health-related proteins from conceptionthrough old age

Ion channels

Other

Cellsignaling

Hormones

Extracellulartransporters

Unknown

Enzymes

Modulatorsof proteinfunction

Receptors

Transcriptionfactors

Intracellularmatrix

Extracellularmatrix

a. Distribution of health-related proteins from conception to birth

Transmembranetransporters

Ion channels

Other

Cellsignaling

Hormones

Extracellulartransporters

Figure 11.4 Proteomics meets medicine. We can categorize genes by their protein products, and chart the relative abundance of each class at different stages of development. The pie chart in (a) considers 13 categories of proteins that when abnormal or missing cause disease, and their relative abundance from conception to birth. The pie chart in (b) displays the same protein categories from conception to old age, plus one activated after birth, the immunoglobulins.

Lewis: Human Genetics: Concepts and Applications, Ninth Edition

III. DNA and Chromosomes 11. Gene Expression and Epigenetics

207© The McGraw−Hill Companies, 2010

Chapter 11 Gene Expression and Epigenetics 205

differentiation of this period. During the prenatal period, enzymes are less abundant, perhaps because the fetus receives some enzymes through the placenta. Immunoglob-ulins appear as a category after birth as the immune system begins to function.

Another way to look at the proteome is by specific functions, which has led to the creation of various “ome” words. Genes whose encoded proteins control lipid synthe-sis, for example, constitute the “lipidome,” and those that monitor carbohydrate production and use form the “glycome.” “Omics” designations are helpful in sorting out the thousands of proteins a human cell can manufacture. However, identify-ing proteins is only a first step. The next hurdle is to deter-mine how proteins with related functions interact—forming “interactomes.”

Gene expression profiles for different cell types under various conditions can provide valuable medical information and are the basis for many new tests that diagnose disease or monitor response to treatment. For example, 55 genes are over-expressed and 480 underexpressed in cells of a prostate cancer that has a very high likelihood of spreading—but not in a pros-tate cancer that will not spread. A test based on such findings assists physicians in deciding which patients can benefit most from further treatment.

insulin—its absence (or the inability of cells to recognize it) causes diabetes mellitus.

Researchers can observe the specialization of pancreas cells by taking individual progenitor cells from human pan-creas ducts or by deriving them from reprogrammed somatic cells (see figure 2.24). Then, by supplying specific growth factors at particular times, the progenitor cells give rise to clusters that look and function like pancreatic islets. When exposed to glucose, the cells secrete insulin! If pancreatic stem cells can be isolated and cultured, it might be possible to coax a person with diabetes to produce new and functional pancreatic beta cells.

Proteomics A more complete portrait of gene expression emerges through proteomics, which considers all proteins made in a cell, tissue, gland, organ, or entire body. Figure 11.4 depicts a global way of comparing the relative contributions of major categories of proteins from conception through birth and from conception through old age.

The differences in proteins produced at different times make sense. For example, transcription factors are more abundant before birth because of the extensive cell

Unknown

Immunoglobulins

Enzymes

Modulatorsof proteinfunctionReceptors

Transcriptionfactors

Intracellularmatrix

Extracellularmatrix

Transmembranetransporters

b. Distribution of health-related proteins from conceptionthrough old age

Ion channels

Other

Cellsignaling

Hormones

Extracellulartransporters

Unknown

Enzymes

Modulatorsof proteinfunction

Receptors

Transcriptionfactors

Intracellularmatrix

Extracellularmatrix

a. Distribution of health-related proteins from conception to birth

Transmembranetransporters

Ion channels

Other

Cellsignaling

Hormones

Extracellulartransporters

Figure 11.4 Proteomics meets medicine. We can categorize genes by their protein products, and chart the relative abundance of each class at different stages of development. The pie chart in (a) considers 13 categories of proteins that when abnormal or missing cause disease, and their relative abundance from conception to birth. The pie chart in (b) displays the same protein categories from conception to old age, plus one activated after birth, the immunoglobulins.

Diseasome

Lewis: Human Genetics: Concepts and Applications, Ninth Edition

I. Introduction 1. Overview of Genetics 13© The McGraw−Hill Companies, 2010

Chapter 1 Overview of Genetics 11

sense—two dozen disorders are much more common in this population. A fourth characteristic of a genetic disease is that it may be “fixable” by altering the abnormal instructions.

Redefining Disease to Reflect Gene Expression Diseases are increasingly being described in terms of gene expression patterns, which is not the same as detecting muta-tions. Gene expression refers to whether a gene is “turned on” or “turned off” from being transcribed and translated into pro-tein (see Reading 1.1).

Tracking gene expression can reveal new information about diseases and show how diseases are related to each other. Figure 1.8 shows part of a huge depiction of genetic disease called the “diseasome.” It connects diseases that share genes that show altered expression. Like most semantic webs that connect information from databases, the diseasome reveals relationships among diseases that were not obvious from tradi-tional medical science, which is based on observing symptoms, detecting pathogens or parasites, or measuring changes in body fluid composition.

Some of the links and clusters in the diseasome are well-known, such as obesity, hypertension, and diabetes. Others are

lower. For example, inheriting one copy of a particular variant of a gene called APOE raises risk of developing Alzheimer dis-ease by three-fold, and inheriting two copies raises it 15-fold. But without absolute risk estimates and no treatments for this disease, would you want to know?

A third feature of single-gene diseases is that they may be much more common in some populations than others. Genes do not like or dislike certain types of people; rather, mutations stay in certain populations because we marry people like ourselves. While it might not seem politically correct to offer a “Jew-ish genetic disease” screen, it makes biological and economic

AutismRett

syndrome DeafnessRetinitis

pigmentosaCataracts

Musculardystrophy

Diabetesmellitus

Heartattack

Alzheimerdisease

Parkinsondisease

Immunedeficiencies

Blood types+

disorders

Schizophrenia

Migraine

Malaria

Dementia

Hypertension

Asthma

Obesity

Braincancer

Othercancers

Anorexianervosa

SeasonalaffectivedisorderObsessive

compulsivedisorder

Coronaryartery

disease

Clottingfactor

deficiency

Othereye

disorders

Connectivetissue disorders

Seizuredisorder

Nicotineaddiction

Mentalretardation

Heartdisease

Figure 1.8 Part of the diseasome. This tool links diseases by shared gene expression. That is, a particular gene may be consistently overexpressed or underexpressed in two diseases, compared to the healthy condition. The lines refer to at least one gene connecting the disorders depicted in the squares. The conditions are not necessarily inherited because gene expression changes in all situations. The diseasome is an oversimplification in several ways. The same symptoms may have different causes, and each condition is associated with expression changes in more than one gene. Shading indicates conditions that may share a symptom. (Based on the work of A-L Barabási and colleagues.)

Table 1.4 How Single-Gene Diseases Differ from Other Diseases

1. Risk can be predicted for family members.

2. Predictive (presymptomatic) testing may be possible.

3. Different populations may have different characteristic disease frequencies.

4. Correction of the underlying genetic abnormality may be possible.

Shared  Gene  Expression

RNA-Chip: Biological Questions

Gene expression analysis (Functional Genomics) Differentiation Responses to environmental factors Disease processes Effects of drugs (Dose/time/class) Identify Genes expressed in different cell types (e.g. Liver

vs Kidney) Learn how expression levels change in different

developmental stages (embryo vs. adult) Learn how expression levels change in disease development

(cancerous vs non-cancerous) Learn how groups of genes inter-relate (gene-gene

interactions) Identify cellular processes that genes participate in

(structure, repair, metabolism, replication, … etc)

Bioinformatics of Microarrays

Array design: choice of sequences to be used as probes Analysis of scanned images

Spot detection, normalization, quantitation Primary analysis of hybridization data

Basic statistics, reproducibility, data scattering, etc. Comparison of multiple samples

Clustering, SOMs, classification … Sample tracking and databasing of results