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CHAPTER 4 CHAPTER 4

Gene, Chromosomes, and Genome G!


Gene, Chromosomes,
IN
and Genome
R N
WA • These lecture notes are mainly based on what the
authors have provided for the textbook.
• Any unauthorized copy or distribution of these
lecture materials is strictly prohibited.
• Please keep these lecture notes only with you and
do not give them out to a third party in any case,
otherwise your misconduct may affect the grade.

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4.0 | Genomics Gets Personal

In the winter of 2003, a baby girl was born who would eventually
become a symbol for the emerging field of personal genomics.

Bea Rienhoff was primarily a healthy baby, but displayed a constellation


of unusual traits, including wide‐set eyes, curled hands and feet, and
poor muscle tone.

Her father, Hugh Rienhoff, a trained geneticist, built a makeshift genetics


laboratory in his home and began a personal project called “The Bea
Project”.

Rienhoff suspected that the mutation existed somewhere in the


TGF‐beta pathway. The biotech company Illumina sequenced the exome
from Bea and family members and found a point mutation in the gene
that encoded for the protein TGF-b3.

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4.1 | The Concept of a Gene as a Unit of Inheritance

An overview depicting several of the most important


https://vimeopro.com/korifeener/bea/video/115936139 early discoveries on the nature of the gene.

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4.1 | The Concept of a Gene as a Unit of Inheritance 4.1 | The Concept of a Gene as a Unit of Inheritance

The earliest studies revealed


genes to be discrete factors that Mendel’s work became the
were retained throughout the life foundation for the science
of an organism and then passed of genetics.
on to each of its progeny.
Mendel crossbred plants
Over the following century, these
through several generations
hereditary factors were shown to
and counted the number of
reside on chromosomes and to
individuals having various
consist of DNA, a macromolecule
characteristics.
with extraordinary properties. Mendel chose to focus on
An overview depicting seven clearly definable
This remarkable journey of He established the laws of
several of the most traits, including plant height
discovery is capped by the inheritance based on his and flower color, each of
important early discoveries
description of the double helical studies of pea plants. which occurred in two
on the nature of the gene.
structure of DNA in 1953. alternate and clearly
identifiable forms.

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4.1 | The Concept of a Gene as a Unit of Inheritance 4.2 | The Discovery of Chromosomes

Mendel’s studies were totally unconcerned with the physical nature


1. Characteristics of organisms are governed by units of inheritance of these elements or their location within the organism.
called genes.
a) Each trait is controlled by two forms of a gene called alleles. By the 1880s, European biologists were using rapidly improving light
b) Alleles could be identical or nonidentical. microscopes to observe newly discernible cell structures.
c) When alleles are nonidentical, the dominant allele masks the Observations of dividing cells by the German biologist Walther
recessive allele. Flemming revealed that the the cell appeared to go to great lengths
2. A reproductive cell (gamete) contains one gene for each trait. to divide the nuclear contents equally between the daughters.
a) Somatic cells arise by the union of male and female gametes.
During cell division, the material of the nucleus became organized
b) Two alleles controlling each trait are inherited; one from each
into visible “threads,” which were named chromosomes, meaning
parent.
“colored bodies.”
3. The pairs of genes are separated (segregated) during gamete
formation. In 1887 the German biologist August Weismann proposed that
4. Genes controlling different traits segregate independently of each meiosis included a “reduction division” during which the chromosome
(independent assortment). number was reduced by half prior to formation of the gametes.

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4.3 | Chromosomes as the Carriers of Genetic Information 4.4 | Genetic Analysis in Drosophila

Chromosomes are present as pairs


of homologous chromosomes. Thomas Hunt Morgan was the first
to use Drosophila (fruit flies) in
During meiosis, homologous genetic research.
chromosomes form a bivalent; then
separate into different cells. Morgan only had available wild type
flies but one he developed his first
Genes on the same chromosome Photograph of a wild-type female fruit
mutant, it became a primary tool for fly and a mutant male that carries a
do not assort independently and genetic research. mutation leading to white eyes.
are part of the same linkage
group. Mutation was recognized as a
mechanism for variation in
Chromosomal behavior correlates populations.
with Mendel’s laws of inheritance.
Sutton’s drawing of the homologous Fruit flies have four
chromosomes of the male grasshopper Studies with Drosophila confirmed
The traits analyzed by Mendel that genes reside on chromosomes. pairs of homologous
that have associated during meiotic chromosomes
occur on different chromosomes. prophase to form bivalents.

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4.4 | Genetic Analysis in Drosophila 4.4 | Genetic Analysis in Drosophila
Crossing Over and Recombination Crossing Over and Recombination

Percentage of recombination
• Crossing Over and between a pair of genes is
Recombination constant.
– Linkage between alleles on
the same chromosome is Percentage of recombination
incomplete. between different pairs of genes
– Maternal and paternal can be different.
chromosomes can
exchange pieces during The positions of genes along the
crossing over or genetic chromosome (loci) can be
recombination. mapped.

Frequency of recombination Simplified representation of


Micrograph of a lily cell: Homologous
indicates distance, and increases a single crossover in a
chromosomes wrap around each other during
meiosis. The points at which the homologues
as distance increases. Drosophila heterozygote
are crossed are termed chiasmata (arrows) and the resulting gametes

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4.4 | Genetic Analysis in Drosophila


4.5 | The Structure of DNA
Mutagenesis and Giant Chromosomes

Exposure to a sub-lethal dose of


X-rays increased the rate of To understand the workings of a
Giant polytene complex macromolecule whether it
spontaneous mutations; inducing
chromosomes is a protein, polysaccharide, lipid, or
mutations became a quicker from the salivary
method to study genes. nucleic acid—it is essential to know
gland of a larval
fruit fly how that molecule is constructed.
Cells from the salivary gland of
Drosophila have giant polytene The mystery of DNA structure was
chromosomes. investigated by a number of
laboratories in both the United
Polytene chromosomes have been States and England in the early
useful to observe specific bands 1950s and was solved by James
correlated with individual genes. SEM of a giant Watson and Francis Crick at
polytene chromosome Cambridge University in 1953.
“Puffs” in polytene chromosomes (Chironomus larva)
allow visualization of gene showing “puffs” Watson and Crick model of DNA
expression.

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Reminder Reminder
4.5 | The Structure of DNA 4.5 | The Structure of DNA

Nucleotides have a polarized structure


where the ends are called 5’ and 3’

Nucleotides are linked into nucleic acids


polymers where sugar and phosphates are
linked by 3’,5’-phosphodiester bonds, and
Electron density model of a DNA Chemical structure of a DNA nucleotide nitrogenous bases project out like stacked
nucleotide containing the base thymine. containing the base adenosine shelves.

• DNA is the genetic material in all organisms. Chargaff established rules after doing base
composition analysis:
• The Structure of DNA: Number of adenine = number of thymine
– The nucleotide is the building block of DNA. Number of cytosine = number of
• It consists of a phosphate, a sugar, and either a pyrimidine or guanine
purine nitrogenous base. [A] + [T] ≠ [G] + [C]
• Two different pyrimidines: thymine (T) and cytosine (C). Chemical structure of a
• Two different purines: adenine (A) and guanine (G). single DNA strand showing
all four nucleotides
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Reminder Reminder
4.5 | The Structure of DNA 4.5 | The Structure of DNA
The Watson-Crick Proposal The Watson-Crick Proposal

The two DNA chains are held


The Watson-Crick Proposal- the together by hydrogen bonds
DNA molecule is a double helix. between each base, and these
chains are complementary to
DNA is composed of two chains of each other.
nucleotides, and these two chains
spiral around each other forming a The double helix makes a turn
pair of right-hand helices. every 10 residues and is 2 nm The Watson-Crick
wide. base pairs
The two chains are antiparallel, they Space-filling
run in opposite directions. Pyrimidines are always paired model of the B
with purines, and only A-T and form of DNA
The sugar-phosphate backbone is C-G pairs fit within double helix.
located on the outside of the
molecule, and the bases are inside Molecule has a major groove EM: DNA released
Schematic representation from the head of a T2
the helix. and a minor groove.
of the DNA double helix bacteriophage

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Reminder Reminder

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Reminder Reminder

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Reminder Reminder

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Reminder

DNA structure
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4.5 | The Structure of DNA
The Importance of the Watson-Crick Proposal

DNA was expected to fulfill three primary


functions:
1. Storage of genetic information. DNA
must contain the information to assemble
all of the proteins that are synthesized by
an organism.

2. Replication and inheritance. DNA


replication allows genetic instructions to
be transmitted from one cell to its
daughter cells and from one individual to
its offspring.

3. Expression of the genetic message.


The information in DNA must be used to
direct which specific amino acids are Three functions required
incorporated into a polypeptide chain. of the genetic material

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4.5 | The Structure of DNA


4.7 | The Complexity of the Genome
The Importance of the Watson-Crick Proposal

DNA is an information repository, which is a property more difficult to


The Watson-Crick model supported the
describe in simple molecular terms than its structure.
notion that information content of DNA
resided in the linear sequence of its All the individuals that make up a species population share the same
bases. set of genes, even though different individuals invariably possess
slightly different versions (alleles) of many of these genes.
A DNA segment would correspond to a
gene, and the sequence would dictate Thus each species of organism has a unique content of genetic
the sequence of amino acids in a information, which is known as its genome.
polypeptide.
For humans, the genome is equivalent to all of the genetic information
Watson and Crick proposed that during that is present in a single (haploid) set of human chromosomes, which
replication, hydrogen bonds of the DNA includes 22 different autosomes and the X and Y sex chromosomes.
helix were broken, causing separation
of the strands. These strands would To understand how the complexity of the genome is determined, it is
serve as a templates for assembly of a first necessary to consider one of the most important properties of the
complementary strand. Three functions required DNA double helix: its ability to separate into its two component strands.
of the genetic material

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4.7 | The Complexity of the Genome 4.7 | The Complexity of the Genome
DNA Denaturation DNA Renaturation

When DNA is dissolved in saline Renaturation or reanneling is when


solution and the solution is slowly single-stranded DNA molecules are
warmed, a temperature is reached capable of reassociating.
when strand separation begins.
In nucleic acid hybridization,
Thermal denaturation (or DNA complementary strands of nucleic
melting) can be monitored by acids form different sources can form
following the increase in absorbance hybrid molecules; this is important in
of UV light by the dissolved DNA. DNA sequencing, cloning, and
amplification.
Temperature where the shift in
absorbance is half completed is the Renaturation of viral and bacterial
melting temperature (Tm). DNA fragments occurs along
A thermal denaturation curve for native
bacteriophage T6 DNA. The “melting” of symmetrical curves, suggesting that
The kinetics of renaturation of
The higher the GC content (%G + the DNA (strand separation) occurs over a these genomes primarily have genes viral and bacterial DNAs.
%C) of the DNA, the higher the Tm. narrow range of temperature arranged in a linear array.

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4.7 | The Complexity of the Genome 4.7 | The Complexity of the Genome
DNA Renaturation DNA Renaturation

Studying reannealing rates of


different genomes has provided
insight into various types of
sequences.

Experiments from plants and animals


show reannealing curves typically
with three broad classes of DNA
sequences.

These classes differ as to the number


of times their nucleotide sequence is
repeated, and are called the highly
Plot of renaturation kinetics for
repeated fraction, the moderately eukaryotic DNA. Reannealing single-
The kinetics of renaturation of repeated fraction, and nonrepeated
viral and bacterial DNAs. stranded DNA usually shows three classes
fraction. of fragments distinguished by their
frequency of repetition within the genome

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4.7 | The Complexity of the Genome 4.7 | The Complexity of the Genome
DNA Renaturation DNA Renaturation: Highly Repeated DNA Sequences

Plot of renaturation Highly Repeated DNA Sequences –


kinetics for eukaryotic represent about 1-10% of total DNA.
DNA. Reannealing single-
stranded DNA usually Satellite DNAs – short sequences
shows three classes of that tend to evolve very rapidly.
fragments distinguished by
their frequency of
repetition within the Minisatellite DNAs – unstable and
genome tend to be variable in the population;
form the basis of DNA fingerprinting.

Microsatellite DNAs – shortest


sequences and typically found in
small clusters; implicated in genetic DNA fingerprinting: DNA is digested
with restriction endonucleases and
disorders.
DNA fragments are size separated by
gel electrophoresis

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Highly repeated DNA sequences


Discovery of satellite DNA
Satellite DNAs Minisatellite DNAs Microsatellite DNAs

Repeated
5-300 bp 12 -100 bp 1-5 bp
unit (bp)
Medium sized-
Very large cluster The shortest cluster
Cluster cluster
size as many as 3000
Up to million bp 10-40 bp in length
repeats
Within the Unstable→ highly
Scattered evenly
centromeres of variable
Localiza- through the DNA
chromosomes (polymorphic)
tion or
character- Distinct satellite
Used to identify Used to analyze the
istics bands during
individuals in evolution in human
density gradient
criminal or paternity populations
centrifugation
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4.7 | The Complexity of the Genome 4.7 | The Complexity of the Genome
DNA Renaturation: Highly Repeated DNA Sequences DNA Renaturation: Highly Repeated DNA Sequences

Early in situ hybridization


studies used radioactively
labelled probe DNA) followed
by autoradiography.

DNA probe hybridized to chromosomes to determine position of satellite sequences FISH can be used to visualize
repetitive sequences like that
found in satellite DNA
In the method of fluorescence in situ hybridization (FISH), fluorescent localized in the centromeric
probes are generated towards a specific DNA sequence in order to regions of the chromosome,
determine its location(s) within the genome of an organism. or for determining the position
of single copy genes. FISH: Chromosomal localization
These probes hybridize to the complementary DNA strands, and the of a nonrepeated DNA sequence
resultant gene/DNA locations are determined from fluorescent ‘spots’
using fluorescence microscopy.

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4.7 | The Complexity of the Genome 4.7 | The Complexity of the Genome
DNA Renaturation: Moderately Repeated DNA Sequences DNA Renaturation: Nonrepeated DNA Sequences

The moderately repeated fraction of the genomes of plants and animals The nonrepeated (or single-copy) DNA sequences include genes that
can vary from 20 to more than 80 percent of the total DNA. exhibit Mendelian patterns of inheritance and localize to a particular site
on a particular chromosome.
This fraction includes sequences that are repeated within the genome
anywhere from a few times to tens of thousands of times. Included within the nonrepeated fraction are the DNA sequences that
code for virtually all proteins other than histones, which comprise less
Some sequences code for known gene products, either RNAs (e.g. than 1.5% of the human genome.
rRNAs) or proteins (e.g. histones), but most sequences lack a coding
function. Even though these sequences are not present in multiple copies, genes
that code for polypeptides are usually members of a family of related
These noncoding elements are scattered (i.e., interspersed) throughout genes, like the globins, actins, myosins, collagens, tubulins, integrins,
the genome and can be grouped into SINEs (short interspersed and most other proteins in a eukaryotic cell.
elements) or LINEs (long interspersed elements).

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4.8 | The Stability of the Genome: Duplication 4.8 | The Stability of the Genome: Duplication
Whole-Genome Duplication (Polyploidization) Duplication and Modification of DNA Sequences

In polyploidization, or whole‐genome
duplication, offspring have four Unequal crossing over
chromosome homologues rather than two. between duplicated genes
provides a mechanism for
Two related species can mate to form a generating changes in
hybrid organism with the combined gene number
chromosomes from both parents, or a 1-
cell embryo can undergo chromosome
duplication and retain the DNA.

The first mechanism occurs often in plants, Gene duplication occurs within a portion of a single chromosome.
and the second often in animals.
A sample of agricultural Duplication may occur by unequal crossing over between misaligned
Polyploidization is common in flowering crops that are polyploid homologous chromosomes.
plants, including numerous crop species
(e.g., wheat, bananas, and coffee).
Duplication has played a major role in the evolution of multigene families.

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4.8 | The Stability of the Genome: Duplication


4.9 | The Dynamic Nature of the Genome: “Jumping Genes”
Evolution of Globin Genes

Examination of globin genes,


whether from a mammal or a fish, Repeated sequences are
reveals a characteristic organization. sometimes present in tandem
arrays, sometimes present on two
Each of these genes is constructed or a few chromosomes, and
of three exons and two introns. sometimes dispersed throughout
the genome.
The globin gene family includes
hemoglobin, myoglobin, and plant Barbara McClintock suggested
leghemoglobin. that genetic elements were
capable of moving around the
Ancestral forms have given rise to genome.
Visible manifestations of
recent forms by duplication, gene
She called this genetic transposition in maize. Kernels of
fusion, and divergence. corn are typically uniform in color.
rearrangement transposition, and
The spots on this kernel result from a
Some sequences, called A pathway for the evolution of the mobile genetic elements mutation in a gene from movement
pseudogenes, resemble globin globin genes. Exons are shown in transposable elements. of transposable elements.
genes but are nonfunctional. red, introns in yellow.

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4.9 | The Dynamic Nature of the Genome: “Jumping Genes”
Maize & transposon Transposons

Only certain sequences can acts as


transposons, but these insert into
target sites randomly.

It requires the enzyme transposase


Dr. Barbara McClintock
to facilitate insertion of transposons
into target site.

Bacterial transposition occurs by


replication of the transposable
element, followed by insertion.

Up to 3% of human genome from


Transposition of a bacterial
transposon element relics.
transposon by a “cut-and
paste” mechanism

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4.9 | The Dynamic Nature of the Genome: “Jumping Genes” 4.9 | The Dynamic Nature of the Genome: “Jumping Genes”
Transposons The Role of Mobile Genetic Elements in Genome Evolution

Integration of the element The two most common families of moderately repeated sequences in
creates a small duplication in human DNA—the Alu and L1 families—are retrotransposons. Alu is an
target DNA, which serves as a example of a SINEs and L1 is an example of a LINEs.
“footprint” to identify sites
occupied by transposable The human genome is estimated to contain about 500,000 copies of L1
elements. (6,000 bp in length), and more than 1 million sites for Alu sequences
(300 bp in length).
Retrotransposons use an RNA
intermediate which produces a Comparative genomic studies indicate that the Alu sequence first
complementary DNA via appeared as a transposable element in the genome of primates about
reverse transcriptase. 60 million years ago and has been increasing in copy number ever
since.
Viruses such as HIV use this
mechanism to replicate their Schematic pathways in the These transposition events generate differences in the locations of Alu
genome. movement of transposable elements. sequences from one person to another and thus contribute to the
DNA transposons and retrotransposons. genetic diversity in the human population.

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4.9 | The Dynamic Nature of the Genome: “Jumping Genes” 4.10 | Sequencing Genomes: The Footprints of
The Role of Mobile Genetic Elements in Genome Evolution Biological Evolution

There are several ways that transposable elements appear to have been
involved in adaptive evolution:
The genomes of hundreds of
1. Transposable elements can carry adjacent parts of the host genome with organisms have been sequenced.
them as they move from one site to another.
In 2004 the “finished” version of
2. DNA sequences originally derived from transposable elements are found the human genome was reported,
as parts of eukaryotic genes and DNA segments that regulate gene revealing that it contains about
expression. Several transcription factors bind to sites in the DNA that 20,000 genes.
arose originally from transposable elements.
Alternate splicing of messenger
3. Transposable elements themselves appear to have given rise to genes.
RNA may account for several
Telomerase, which plays a key role in replicating the DNA at the ends of
proteins from one gene.
chromosomes, may be derived from a reverse transcriptase encoded by
an ancient retrotransposon.
Post-translational modifications
4. A number of recent studies have found evidence that mammalian brain also account for different protein
cells have a greatly elevated level of L1 retrotransposition compared to functions.
that of other tissues. Genome comparisons

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4.11 | Comparative Genomics:


4.12 | The Genetic Basis of “Being Human”
“If It’s Conserved, It Must Be Important”

Since most intergenic and intronic sequences tend to change rapidly By focusing on conserved sequence, we
as organisms evolve, these sequences tend not to be conserved. can learn about traits we share with
other species.
In contrast, genome regions that encode protein sequences or contain
regulatory sequences that control gene expression are subject to The gene FOXP2 in human differs very
natural selection, which tends to eliminate individuals whose genome little from that in chimps, and is called
contains mutations. the “speech gene”.

If these sequences tend to be conserved, the best way to identify Another gene is HAR1, which also differ
functional sequences is to compare the genomes of different types of little between humans and chimps and
organisms. its function is unknown.
Duplication of the
Recent studies have shown a significant proportion of functional DNA The gene AMY1 encodes the enzyme amylase gene during
sequences are constantly evolving and are not highly conserved. amylase and its frequency is remarkably human evolution: chimp
Focusing on just conserved sequences carries a risk of missing many different between humans and chimps. (top; single copy) and
human (bottom; multiple
of the most important functional elements in the genome.
copy)

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4.13 | Genetic Variation within the Human Species Population
4.13 | Genetic Variation within the Human Species Population
DNA Sequence Variation

Since the completion of sequencing from the Human Genome Project The most common type of genetic variability in humans occurs at
sequence, a great deal of attention has been focused on how DNA sites where single nucleotide differences are found in a population.
sequence varies within the human population.
When present in at least 1 percent of the population, these sites
Genetic polymorphisms are sites in the genome that vary among are called single nucleotide polymorphisms (SNPs) and occur
different individuals, and usually refers to a genetic variant that occurs as two alternate alleles, such as A or G.
in at least 1 percent of a species population.
On average, two randomly selected human genomes have about 3
million single nucleotide differences between them, or one every
The concept of genetic polymorphisms began with the discovery in
thousand base pairs.
1900 by an Austrian physician, Karl Landsteiner, that people could
have at least three alternate types of blood, A, B, or O. This is a result Current estimates suggest that each person harbors over 100 rare
of members of the population having different alleles of a gene single nucleotide variants in his or her exome (the portion of the
encoding a sugar-transferring enzyme. genome that codes for proteins).

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4.13 | Genetic Variation within the Human Species Population 4.13 | Genetic Variation within the Human Species Population
Structural Variation Copy Number Variation

Segments of the genome can change The lengths of minisatellite sequences depend on the number of
as the result of duplications, deletions, copies of the sequence that are present at particular sites in the
insertions, and inversions. chromosomes, an example of a copy number variation (or CNV).

Large changes range from hundreds to Larger-sized CNVs (<1 kb) affect approximately 10–15 percent of the
millions of base pairs in length and are human genome, including large numbers of protein-coding genes.
called structural variants.
Many carry extra copies of one or more genes that encode important
Intermediate-sized structural variants physiological proteins, generally associated with overproduction of a
are much more common than protein. A significant number of persons who develop early-onset
previously thought. Alzheimer’s disease possess extra copies of the APP gene.

A typical human genome carries In some cases, extra copies of a gene can be beneficial, as illustrated
approximately 1000 structural variants, Structural by the repeated duplication of the amylase gene (AMY1), which has
variants. been found in certain human populations that have a high starch
ranging in length from about 500 bases
Schematic and content in their diet.
to 1.3 million bases (Mb). inversion viewed
microscopically
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| The Human Perspective | The Human Perspective
I. Diseases That Result from Expansion of Trinucleotide Repeats II. Application of Genomic Analysis to Medicine

Until recently, the gene responsible


for a disease was identified through
traditional genetic linkage studies.

However, the low penetrance of most


• Mutations occur in genes containing a repeating unit of three nucleotides. genes for common diseases cannot
• The mutant alleles are highly unstable and the number of repeating units tends be identified through family linkage
to increase as the gene passes from parent to offspring.
studies.
• Type I disease are all neurodegenerative disorders resulting form expansion of
CAG trinucleotides.
Genome-wide association studies
• Huntington’s disease (HD) result from ≥ 36 glutamine repeats in the huntingtin
gene. (GWAS) look for links between a
• The molecular basis of HD remains unclear but it is presumed that expanded disease and polymorphisms located The genome is divided into haplotypes
glutamine repeats are toxic to brain cell. in the genome.
• Type II diseases arise from a variety of trinucleotide repeats, and are present in
parts of the gene that do not code for amino acids (i.e. fragile X syndrome).

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| The Human Perspective


II. Application of Genomic Analysis to Medicine

SNPs may play an important


role is susceptibility to disease
or act as genetic markers for
susceptibility.

SNPs can be inherited in blocks


called haplotypes.

Haplotype maps (HapMaps) are


based on common haplotypes.

HapMaps may lead to


associations between disease The genome is divided into haplotypes
and haplotypes.

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