Mutation and instability of Human DNA R' D' Gietz Chapter 9

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Mutation and instability of Human DNAR. D.
GietzChapter 9

• Learning Objectives
• 1. To understand the types of changes in DNA
  that can occur in DNA.
• 2. To understand the difference between
  transition and transversion mutation.
• 3. Understand how mutations can be classified.
• Understand why mutations occur more frequently in
  males.
• Understand the mechanism that can cause certain
  types of mutation

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• Mutation is a heritable change in the genome.
• There are many different classes of change.
• Base substitutions
• All types
• Common in coding and non-coding DNA
• Transition and Transversion
• Transitions are more common that transversion
• Synonymous and non-synonymous
• Synonymous are more common
• Gene conversion-like events
• Rare except at certain tandemly repeated loci or
  clustered repeats

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• Insertions
• One or a few nucleotides
• Very common in noncoding DNA but rare in coding
  DNA where they produce frameshifts
• Triplet expansion
• Rare but contribute to several disorders
• Large insertions
• Rare but get large scale tandem duplications and
  transposible elements
• Deletions
• One or a few nucleotides
• Very common in non-coding DNA but rate in coding
  regions as they produce frameshifts
• Larger deletions
• Rare but get large scale tandem repeats deletions
  and transposible elements

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• Chromosome abnormalities
• Numerical
• Rare as constitutional mutations but can often
  be pathogenic
• Structural
• More common as somatic mutations and often
  associated with tumor cells.

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The type of cell that a mutation occurs is also
important. If a mutation occurs in a somatic
cell CANCER may develop. However if the mutation
occurs in a germ cell it can be passed on to the
next generation. Mutations occur at a very low
frequency. So most of the variation that is
found in the genome of a one individual is due to
inherited changes and not de novo
mutations. Mutation is usually associated with
deleterious effects on phenotype. Changes at the
DNA and protein level that are not obviously
deleterious to phenotype are refered to as
polymorphisms. Allelic variation is referred to
as polymorphism. In fact the amount of variation
in the human genome is quite high. 1 in 250 to
1 in 1000 bases are different between alleles.
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Simple mutations Mutation can occur due to
errors in replication and repair of DNA.
Replication errors occur at frequency of 10-9 to
10-11. Adult human needs 1017 cell divisions to
produce 1014 cells each new cell needs to
incorporate 6 x 109 new nucleotides complete
fidelity needs 6 x 1026. The average coding
region for a gene is 1.7 kb this means that the
average frequency of mutation per gene per cell
division is 1.7 x 10-6 to 1.7 x
10-8.
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• TRANSITION mutations
• substitution of a purine (A or G) for another
  purine OR substitution of a pyrimidine (C or T)
  for another pyrimidine .
• TRANSVERSION mutations
• substitution of a purine (A or G) for a
  pyrimidine of vice versa.
• A lt--gt C These ?? are Transitions
• ??????????????????
• G lt--gt T These lt--gt are
  Transversions
• Theoretically transversion should be 2 x more
  frequent than transitions. Transitions occur 1.4
  times more frequently than transversions. Due to
  C-gtT transition due to 5-m C deamination. CpG
  has a mutation rate 8.5 times higher than any
  other dinucleotide.

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Mutations are generated randomly in DNA, however
only 3 of the DNA codes for products. Mutations
in coding regions are classified as Silent
(synonymous) do not change the product,
therefore are neutral. Nonsynonymous mutations
that result in a change in the protein or
functional RNA. Most nonsynonymous mutations are
deleterious, causing problems in the products
produced. This can result in disease or
lethality. Nonsense mutations, Missense
mutations The location of base substitutions in
coding DNA is non random. Why? Due to selection
pressure on the base change. Natural selection
is the process by which mutational changes are
fixed or eliminated from the population.
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Mutations in Coding DNA If one analyzes the
mutations in coding DNA we see that they are non
random. Due to the way the genetic code is set
up there is redundancy that makes certain codons
less susceptible changes in the protein product.
See below
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Rate of nucleotide substitution vary depending on
the position in the genome as well as in genes.
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Rates of Synonymous and non synonymous mutations
are not the same genome wide. It depend on the
selective pressure for that specific gene!
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Mutation rate is higher in males. It has been
observed that many mutations are derived
paternally. In some cases 4.5 to 8.5 times as
high. This is due to the higher number of cell
divisions that are necessary for the production
of sperm.
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Examples of genes that show an increase mutation
rate from paternal sources.
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Slipped strand Misspairing Causes Deletions
and Insertions During DNA Replication.
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Other mechanisms for tandem repeat expansion or
contraction.
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Unequal crossover can lead to homogenization. DNA
sequences can be homogenized by unequal crossing
over.
Tandem duplication can occur by unequal sister
chromatid exchange
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Gene conversion is the non reciprocal exchange
between alleles. It can occur between alleles on
homologous chromosomes or in rare cases between
two different related loci.
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Mutation can affect function in a number of ways
Examples of mutations that affect gene function
---gt
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Mutation can affect function in a number of ways
Examples of mutations that affect gene function
---gt
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Mutations that affect splicing Mutations can
affect each process involved in the flow of
information from DNA to proteins. Here we see
that mutants can affect the process of splicing
add or deleting information into the mature mRNA.

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Example of a mutation that affect splicing LGMD2A
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Creation of a cryptic splice site.
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Repeated elements

• Tandem repeats are found through out the genome.
  
• Give rise to various types of mutation
• See Table 9.6
• deletions and duplications and some inversions as
  well as insertions (retroviral)

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Deletions due to short tandem repeats.
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Triplet types
Triplet repeat expansion Uninterrupted triplets
are more prone to expansion that those
interrupted by other sequences
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VNTRs Variable number tandem repeats are
important in disease. They can contract or
expand, but expansion is usually what is seen in
certain disease states. Slipped strand
mispairing is one of the mechanisms that can lead
to changes in VNTR numbers.
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Deletions or Duplications can be due to
recombination or
Gene conversion 25 mutations Involve
deletions The rest are gene Conversions.
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Mutations in the 21-hydroxylase gene suggest gene
conversion as the mechanism of mutagenesis.
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Direct repeats have been shown to be involved in
deletions Due to recombination in mutation in the
human mitochondrial DNA. Due to slipped strand
misspairing
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Recombination is hypothesized to have produced
this Mutation in the factor VIII gene that was
identified in one patient.
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Summary 1

• Variation is due to multiple mechanisms
• Single bases, -gt DNA replication, DNA damage
• Multiple bases,-gt DNA replication,
  Recombination, gene conversion, DNA damage
• Changes can be Synonymous or non-synonymous for
  their effect in proteins. Selection acts at this
  level.
• Males have higher mutation rate due to more cell
  divisions DNA replication

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Summary 2

• Repeated elements expand and contract by
  slipstrand misspairing or unequal crossing over.
• Mutations can occur in many different parts of a
  gene and give rise to different severities.
  Mutations affecting splicing also affect the
  protein.
• Recombination and gene conversion can give rise
  to changes in the genetic material, some that are
  deleterious.