Download Human Genetic Variation

Human Genetic
Variation
Motivation to study
human genetic variation
„ Intellectual interests: evolution of our species and its
history.
„ Medical importance: there is a genetic component to
Javad Tavakkoly Bazzaz MD, PhD
[email protected]
many diseases, esp. more common complex disorders
such as diabetes, cancer, cardiovascular, and
neurodegenerative.
„ Pharmaceutical: genetics will determine an individual’s
response to a drug.
Convergent Evolution
Why is phenotypic variation not as important?
„ Phenotypic variation is the result of:
¾Genotypic variation
¾Environmental variation
¾Other effects
come to resemble one another if they live in very
similar environments.
„ Example:
8Such as maternal or paternal effects
„ Not completely heritable!
Potential Topics:
I. Evolution of Gene Expression
II. Evolution of transcriptional regulatory code
III. Evolution of regulatory networks
IV. Evolution of duplicate genes
IV. Emergence of new genes
V. Protein Protein interactions
VI. Genetic variation within and between species
VII. Effects of recombination and gene conversion on GC
content and substitution rate
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„ Species from different evolutionary branches may
1. Ostrich (Africa) and Emu (Australia).
2. Sidewinder (Mojave Desert) and
Horned Viper (Middle East Desert)
Evolution of Gene Expression
Examine how gene expression has diverged
between species (or between duplicate
genes).
A study may examine only changes in
expression but not changes in regulatory
sequences.
There have been many studies on this topic.
Emergence of new genes
The Paradox of Variation:
Evolution requires variation, but
natural selection eliminates variation.
Hardy-Weinberg Principle
„ The concept that the shuffling of genes that
occur during sexual reproduction, by itself, cannot
change the overall genetic makeup of a
population.
Hardy-Weinberg Principle
„ This principle will be maintained in nature only if all five
of the following conditions are met:
1. Very large population
2. Isolation from other populations
3. No net mutations
4. Random mating
5. No natural selection
„ Remember:
If these conditions are met, the population is at equilibrium.
This means “No Change” or “No Evolution”.
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HWE: 5 violations
Hardy-Weinberg Principle
„ So, five ways in which populations CAN evolve!
„ Mutation
„ Nonrandom mating
„ Migration (Gene flow)
„ Small population sizes (Genetic drift)
„ Natural selection
p2 + 2pq + q2 = 1
„ Describes a population which is:
¾large
¾Panmictic (no group structures or mating
restrictions
¾not undergoing natural selection
¾not subject to gene flow from other pop’ns
Random mating
„ Under random mating, the chance of any individual in a
population mating is exactly the same as for any other
individual in the population
Mechanisms that change
gene or genotype frequencies
„ natural selection
„ Generally, hard to find in nature
„ genetic drift
„ But, can approximate in many large populations over
„ bottlenecks and founder effects
short periods of time
„ inbreeding
„ assortative mating
Non-random mating
„ Violations of random mating lead to changes in genotypic
frequencies, not allele frequencies
„ But, can lead to changes in effective population size…
Non-random mating
„ Reduction in the effective population size leaves a door
open for the effects of…
„ Genetic Drift!
„ Drift is the effect of chance occurrences on the
genotype frequencies of a population
„ Greater effect in small populations than large
populations
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Genetic Drift
Genetic Drift
„ Change in the gene pool of a small population
due to chance.
„ Bottlenecks:
„ Founder effect:
What happens when a population is started with only a
few individuals from a larger population
„ The chances of being represented in the new
population are related to the frequency in the original
population
„ BUT, chance plays a role, as DRIFT
„ Instead of founding a new population, the whole
population is drastically reduced in size (e.g. by a
tornado or hurricane); chances of being represented
in the population are based on frequencies before
the catastrophe
Bottleneck Effect
Genetic bottlenecks and founder effects
„ Genetic drift (reduction of alleles in a population)
resulting from a disaster that drastically reduces
population size.
„ Examples:
catastrophe
or
colonization
event
1. Earthquakes
2. Volcano’s
Founder Effect
„ Genetic drift resulting from the colonization of a
new location by a small number of individuals.
„ Results in random change of the gene pool.
„ Example:
Islands (first Darwin finch)
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„ Migration = Gene Flow
„ Definition: The migration of individuals (and their alleles)
from one population to another
„ Gene flow is the flow of alleles between populations
Mechanisms that maintain genetic diversity
„ Heterozygote advantage
„ Frequency-dependent selection
„ Gene flow from other populations
„ Genotype-environment interactions
Heterozygote advantage
„ Cystic fibrosis
¾ nonfunctional chloride channels
8 normal chloride channels funnel water out of cell
¾ thick, dry mucus in lungs and intestines
¾ mutation is 52,000 yrs old
„ Possible heterozygote advantage
¾ heterozygotes have half as many working
chloride channels
¾ lose half as much water during about with
cholera or other infections
Sources of genetic variation (during meiosis)
Reassortment of genetic material (during meiosis)
„ Chromosomal reassortment; a human has 23 pairs of
chromosomes, one of each pair is inherited from the
father, and the other one from the mother.
„ Mutation; errors in DNA copying. This may result in
SNPs or also larger portions of DNA may be duplicated
or copied incorrectly.
„ Genetic recombination; shuffling of segments between
partner chromosomes of a pair.
Molecular Biology of the Cell, Alberts et al.
Garland Publishing 2002 (Fig. 20-8)
Other types of genetic variations…
Single Nucleotide Polymorphisms (SNPs)
„ Major source of genetic variation.
„ Estimated approx. 7 million SNPs that occur with
frequencies at least 5% in the human population;
approx. 11 million with frequencies at least 1%.
„ Can we determine the associations between these
variants and diseases?
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Mutation
Genetic variation
„ The human genome has approximately 10 million
polymorphisms, i.e. genetic variants that occur at the
level of about 1% or more in the population.
„ Many of these polymorphisms are SNPs, single
„ Mutation is the source of genetic variation!
nucleotide polymorphisms.
„ These polymorphisms contribute to our individuality, and
„ No other source for entirely new alleles
also influence our susceptibility to various diseases.
Rates of mutation
„ Vary widely across:
Rates of mutation
„ Measured by phenotypic effects in humans:
¾Rate of 10-6 to 10-5 per gamete per generation
¾Species
„ Total number of genes?
¾Genes
¾Loci (plural of locus)
¾Environments
¾Estimates range from about 30,000 to over
100,000!
¾Nearly everyone is a mutant!
Rates of mutation
„ Mutation rate of the HIV–AIDS virus:
Rates of mutation
„ Rates of mutation generally high
¾One error every 104 to 105 base pairs
„ Size of the HIV–AIDS genome:
¾About 104 to 105 base pairs
„ Leads to a high load of deleterious (harmful)
mutations
„ So, about one mutation per replication!
„ Sex may be a way to eliminate or reduce the
load of deleterious mutations!
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Types of mutations
„ Point mutations
Types of mutations
„ Gene duplication
¾Base-pair substitutions
¾Result of unequal crossing over during meiosis
¾Caused by chance errors during synthesis or
¾Leads to redundant genes
repair of DNA
¾Leads to new alleles (may or may not change
phenotypes)
Types of mutations
„ Chromosome duplication
8Which may mutate freely
8And may thus gain new functions
Effects of mutations
„ Relatively speaking…
¾Caused by errors in meiosis (mitosis in plants)
¾Common in plants
8Leads to polyploidy
8Can lead to new species of plants
ÁDue to inability to interbreed
How can mutations lead to big changes?
„ Accumulation of many small mutations, each with
a small effect
„ Accumulation of several small mutations, each
with a large effect
„ One large mutation with a large effect
„ Mutation in a regulatory sequence (affects
regulation of development)
„ Most mutations have little effect
„ Many are actually harmful
„ Few are beneficial
What Does It Mean?
„ Any permanent heritable genetic change in the genome
called mutation
„ Importance:
¾ Source of genetic polymorphism
¾ Driving evolution
¾ Causes of many human disorders
„ Sources of mutations:
¾ Endogenous mutations: the greatest source
¾ Exogenous causes: environmental mutagens
„ Classification:
¾ Many different basis for classification
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Causes of Mutations
„ Endogenous causes : most common
¾ Depurination: 5000 adenine or guanine loss per day in each
nucleated human cell
¾ Deamination: the net effect is C º T transition
8 around 100 cytosines deaminate per day per human cell to produce
uracil
¾ Reactive oxygen: attack purine and pyrimidine rings
¾ DNA replication errors: nt mismatched due to incorrect
proofreading
¾ Mistake in recombination & …..
„ Exogenous causes:
¾ Chemical mutagens
¾ Physical mutagens
Definitions and Terminology
„ Evolution:
¾ the change in genotype frequencies over time
„ Microevolution
¾ Changes within populations or species in gene
frequencies and distributions of traits
„ Macroevolution
¾ Higher level changes, e.g. generation of new species
or higher–level classification
Microevolution
Macroevolution
„ A change in a population’s gene pool over a secession
„ Any evolutionary change above the level of species origin of
of generations.
„ Evolutionary changes in species over relatively brief
periods of geological time.
taxonomic groups higher than the species level.
„ Macroevolution’s subject matter includes the origins and fates of
major novelties such as tetrapod limbs and insect wings, and the
impact of continental drift and other physical processes on the
evolutionary process. With its unique time perspective,
paleontology has a central role to play in this area: the fossil
record provides a direct, empirical window onto large-scale
evolutionary patterns, and thus is invaluable both as a document
of macroevolutionary phenomena, and as a natural laboratory
for the framing and testing of macroevolutionary hypotheses.
Depurination, Deamination
„ Depurination & Deamination
Molecular
Mechanisms in
Genetic Changes
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Exogenous Mutagens
„ Exogenous causes of DNA damage
Classification of Mutations
„ Mutations are classified on different basis:
¾ On the basis of affected cells
8 Somatic mutation
8 Germline mutation
¾ Due to the level of change in the genome
8 Genome mutation
8 Chromosome mutation
8 Gene mutation
Classification of Mutations
Gene Mutations
„ Gene mutations can be grouped into different classes
„ An important classification is on the basis of the mutation
effect on the gene function
¾ Gain of function mutations
8 Mutational homogeneity
¾ Loss of function mutations
8 Genetic heterogeniety
according to the effect on the DNA sequence:
¾ Base substitutions (mainly single base)
8 Silent
8 Nonsense
8 Missense
¾ Deletions
¾ Insertions
„ Every one of the above classes may be categorized as:
¾ Simple mutations: involve just a single DNA sequence
¾ Sequence exchange mutations: involve exchanges
between two allelic or nonallelic sequences
Simple Mutations
„ Main cause of simple mutations: errors in DNA replication and
repair
¾ How big is this treat?
¾ Frequency of uncorrected replication errors: 10 -9 - 10 -11 per
incorporated nucleotide
¾ Human genome: 6 x 10 9 nucleotides
¾ Adult human: 1014 cells, around 1016 - 1017 cell division life time
¾ So: 50 billions mutations during this class
¾ Average human gene: 1.65 kb so:
¾ Average mutation frequency / gene / cell division: 1.65 x 10-6 10-8
¾ During human lifetime (1016 mitosis) each gene collects about
108 - 1010 mutations
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Facts About Simple Mutations
„ Frequency of base substitutions is nonrandom according
to substitution class
„ Frequency of mutations in noncoding DNA is higher than
coding DNA
„ The location of base substitutions in coding DNA is
nonrandom
„ Amino acids have different degree of mutability
„ Substitution rates vary between different genes and
between different gene components
„ Substitution rate can vary in different chromosomal
regions and in different lineages
Facts About Simple Mutations
„ Frequency of base substitutions is nonrandom according
to substitution class
¾ Comparing transition vs transversion rate
¾ Statistically transversions is expected to be twice as
frequent as transitions
¾ Comparison of orthologs (DNA molecules that share a
common origin) showed an unexpected higher
transition rate in mammalian genomes
Transition vs Transversion
„ Comparison of 337 pairs of human and rodent orthologs
by Collins and Jukes, 1994 showed:
¾ 1.4/1 ratio of transition to transversion for substitutions
with no amino acid change
¾ 2/1 ratio, with amino acid change
„ Why is that for?
¾ High frequency of C ÖT transitions (at CpG
dinucleotide) (CpG: hotspot of mutation, 8.5 times
higher than average dinucleotide mutation rate)
¾ sequence-dependent proofreading activities of the
DNA polymerase
Base Substitutions in Coding DNA
Degenerate Base Positions
„ The location of base substitutions in coding DNA is
nonrandom
„ Base positions in amino acid-specifying codons are
grouped into three classes:
¾ Nondegenerate sites: 65%
¾ Fourfold degenerate sites: 16%
¾ Twofold degenerate sites: 19%
„ Amino acid mutability: depends on the physiologic effect
of the amino acid (mainly its side chain)
¾ Cysteine: less mutable
¾ Serine and threonine: higher mutability
Relative Amino Acid Mutability
Substitution Rates in Different Genes
„ Substitution rates vary considerably between different
genes
„ Variation is much more among non-silent positions
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Substitution Rate & Gene Components
Substitution Rate & Gene Components
„ Substitution rates vary between different gene
„ Substitution rates vary considerably between different
components
¾ Overall genome wide sequence identity between
orthologs is estimated around 69.1%
¾ Coding regions are the most conserved (85%
sequence identity between orthologs)
¾ This is 68.6% for Introns
¾ 75.9% for 5’ UTR
¾ 74.7% for 3’ UTR
¾ 73.9% for promoters (200 bp upstream)
¾ 70.9% downstream 200 bp
Substitution Rate & Chromosomes
„ Substitution rates vary among different chromosomes
¾ X chromosome: lowest substitution rate (number of
germ cell divisions in males and females)
¾ Chromosome 19: Highest (see below)
¾ Mitochondrial genome has much higher substitution
rate than nuclear genome
gene components
Substitution Rate/Chromosomal Regions
„ Substitution rates vary among different chromosomal
regions
„ There is a correlation between substitution rate,
recombination rate and also SNP density
Substitution Rate/Different Lineage
„ Comparison between mouse and human
¾ Substitution rate is much higher in mouse (2.2 x 10-9
in human vs 4.5 x 10-9 in mouse)
¾ Both species showed a net loss of nucleotides which
is at least twice as high in mouse
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Genetic Mechanisms Causing
Sequence Exchange Between
Repeats
Slipped Strand Mispairing
„ Slipped strand
mispairing can cause
deletion or insertion into
microsatellite loci (short
tandem repeats)
„ It can occur during
replication (replication
slippage or polymerase
slippage) or in
nonreplicating DNA
Creation of Fusion (Hybrid) Genes
„ Homologous equal crossover between alleles on
nonsister chromatids can generate novel fusion (hybrid)
genes
Ins/Del in UEC and UESCE
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Unequal Crossover
„ Homologous recombination: is the recombination
(crossover) between identical or very similar DNA
sequences, and usually involves breakage of nonsister
chromatids and rejoining of the fragments
„ Unequal crossover (UEC): nonallelic homologous
recombination in which the crossover takes place
between nonallelic sequences on nonsister chromatids
„ Sister chromatid exchange: is an analogous type of
sequence exchange involving breakage of individual
sister chromatids and rejoining fragments
„ Unequal sister chromatid exchange (UESCE)? …..
Consquences of UEC and UESCE
„ UEC and UESCE occur predominantly in regions with
tandem repeats of moderate to large size sequence with
high homology between the repeats
„ UEC and UESCE can cause insertions and deletions
„ UEC and UESCE can also occur by mispairing between
repeats which are separated by a considerable amount of
intervening sequence (short interspersed repeats, eg. Alu
repeats) causing tandem gene duplication
„ UEC in a tandem repeat array can result in sequence
homogenization
Tandem Gene Duplication in UEC/UESCE
Sequence Homogenization in UEC
Nonreciprocal Sequence Exchange
„ Nonreciprocal sequence exchange is the transfer of DNA
sequence between a pair of nonallelic DNA sequence
(interlocus gene conversion) or allelic sequences
(interallelic gene conversion) [a directional sequence
exchange]
„ Here the donor strand remains unchanged
„ And the acceptor strand changes
„ One possible mechanism for this is formation of a
heteroduplex between the donor strand and acceptor
strand and conversion of the acceptor strand by
mismatch repair DNA repair system
Nonreciprocal Sequence Exchange
„ Interallelic vs Interlocus
Mechanism of NSE
Splicing Mutations
„ These are mutations causing changes in splicing pattern
of mRNA
„ Mechanisms:
¾ Alteration of conserved splice signals
¾ Activation of cryptic splice sites
„ Consequences:
¾ Intron retention
¾ Exon skipping
¾ Extension or shortening of exon
Splice Mutations
The mtDNA, A Mutation Hotspot
„ High rate of mitochondrial disorders (unexpected)
„ There is a high rate of muation in mtDNA
„ Reasons:
¾ 93% of mtDNA is coding DNA
¾ No protection by histones
¾ Lack of adequate DNA-repair mechanism
¾ Many round of replication
¾ Bottleneck effect may also fix the mutation in mtDNA
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