W3LECT - GENETIC VARIATIONS Flashcards
What are classic definitions of Mutation and polymorphism?
- Mutation
- Disease causing variation
- Rare variation - Polymorphism:
- Variation with a population frequency of > 1%
- Non-harmful or neutral variation
What are the differences between mutation and polymorphism?
- Mutations are sudden heritable changes in the DNA
- Polymorphism: DNA variation with a known population frequency (can be used in population genetic studies). There is no frequency limit
*** It is proposed that in most cases, instead of mutation and polymorphism neutral terms like “sequence variant”, “alteration” and “allelic variant” should be used.
What are the most frequent variants?
SNP/SNV: single nucleotide polymorphism/variations
E.g,
* CAGGATAGGCATG
* CAGGATTGGCATG
What are Structural variations?
Copy number variation (CNV)
- range from about one kilobase to several megabases in size.
- Genes may be involved.
- Phenotypic consequences may occur.
≈ 9–15% of heritable variation in gene expression is due to copy number variation.
What are Differences between human genomes?
- 0.1% in SNP/SNVs
- 0.4% in CNVs
=> Altogether: 0.5% - Between individuals, separated historically long ago from each other, the difference can be as high as 2-3%.
- Large genomic rearrangements
Can monozygotic twins differ in CNVs?
Monozygotic twins can differ in CNVs.
=> Mutation rate can be high!
By the cause, mutations may be __- (2 things)
- Spontaneous
- Induced by mutagenic agents
What are the mutation hot spots?
CpG islands
=> In mammals 70% of CpG cytosines are methylated (regulation of DNA functions, see epigenetics)
List the causes of these DNA damage
- Radio- and chemo- therapy
- UV-light
- Replication errors
- Alkylating agent
- ROS
What are the results of these DNA-damage causes
- Double strand break
- Helix distorting damage
- Mismatch, deletion, insertion
- O6 - alkyl - guanin
- Single-strand break
Name these repair systems
- DSB repair system
- Nucleotide excision repair
- Mistmatch repair
- Direct reversal
- Single-strand break repair
- Base excision repair
Name these types of DNA damage
- Double strand helix break
- Helix distorting
- Mistmatch, deletion, insertion
- O6 - alkyl - guanin
- Single-strand break
Cell Cycle Checkpoints
1. What is the role of metaphase checkpoint?
Check for:
- Chromosome spindle attachment
Cell Cycle Checkpoints
2. What is the role of G2 checkpoint?
Check for:
- Cell size
- DNA replication
Cell Cycle Checkpoints
3. What is the role of G1 checkpoint?
Check for:
- Nutrients
- Growth factors
- DNA damage
Diseases caused by errors in the DNA repair
1. What are the examples of Diseases caused by errors in the DNA repair
- ATM = Ataxia telangiectasia
- Li-Fraumeni syndrome
Diseases caused by errors in the DNA repair
2. Describe ATM = Ataxia telangiectasia
- Mutation in ATM causes rare, neurodegenerative, inherited disease (AR), that affects many parts of the body and causes severe disability, characterized by radiosensitivity and different tumors.
- Telangiectasias, also known as spider veins, are small dilated blood vessels near the surface of the skin
Diseases caused by errors in the DNA repair
3. Describe Li-Fraumeni Syndrome
- Characterized by development of multiple cancers throughout one’s life.
- Inheritance: Autosomal dominant
- Gene: TP53
- Lifetime risk of cancer
DNA repair mechanisms
1. What are the 2 DNA repair mechanisms?
- Direct repair
- Excision repair
DNA repair mechanisms
2. What are the characteristics of repair mechanisms?
- Repair mechanisms: nuclear but not mitochondrial DNA
- During life more mutations are accumulated in the mitochondrial DNA which is one of the mechanisms of aging
DNA repair mechanisms
3. Describe direct repair
- the change is reversed
- no template is needed
- mainly in prokaryotes
DNA repair mechanisms
4. Describe excision repair
- template is needed
- in eukaryotes
How does Correction of DNA errors occur?
- DNA polymerase with with proofreading ability
- Mismatch repair
Name of the disease caused by the defective nucleotide excision repair enzymes
Xeroderma pigmentosum
Describe Lynch syndrome
- Hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch syndrome is caused by failure in mismatch repair
- Autosomal dominant
- 7 different genes
- Earlier (44 y) than non-hereditary colon cancer
- One of the most frequent inherited disorder
How do we Repair double strand breaks (DSB)?
What are the characteristics of Somatic mutations?
- Arise in somatic cells
- Passed on to other somatic cells but not to next generation
- Effect of these mutations depends on the cell type & the developmental stage of the organism
- The majority of cancer is caused by somatic mutations.
- Usually several mutations are needed for tumor development.
What are the 2 types of somatic mutations?
- Driver mutation: confers a selective growth advantage
- Passenger mutation: has no effect on the fitness of a clone
Describe driver mutations
Driver mutations in:
- Oncogenes
- Tumor suppressor genes
Describe Germ line mutations
- Inherited from one generation to the next one
- Mutations (base substitution, deletion, etc.) during DNA
synthesis before meiosis
+) Each new born gets about 60-80 new point mutations from their parents. More from father.
+) More STR mutations: mutation rate of STR is higher (6,9×10-4 /locus/generation vs. SNV: 10-8 /generation - Chromosomal mutations
Localization and consequence of mutations
1. What are the consequences if mutations happen in region 1, 2, 3?
1/ Promoter mutations
-> changed transcription
2/ Exon mutations
-> amino acid change or truncated protein (stop)
3/ Intron mutations
-> errors in splicing or in regulation
Localization and consequence of mutations
2. What are the consequences if mutations happen in region 4, 5, 6?
4/ Polyadenylation site mutations
-> decreased mRNA stability
5/ 5’ UTR -> decreased protein synthesis
6/ 3’ UTR → disturbed translation and localization
- Mutations of other regulatory sequences (enhancers, silencers) also may influence (usually decrease)transcription.
What happen if there is Mutation in splice site?
> 98% of introns: 5’: gt (splice donor), 3’ ag (splice acceptor)
=> They are recognized by the splicing machinery
What happen if there loss of the splice donor?
Loss of the splice donor for the second intron causes the
splicing machinery to use the prior splice donor.
=> This causes
exon 9 to be spliced to exon 11, entirely omitting exon 10
How do we classify mutations by the function?
- Gain-of-function mutations
- Loss-of-function mutations
- Exceptions:
+) Haploinsufficiency
+) Dominant negative mutations
=> These mutations are also expressed in heterozygotes
so in both cases the effects are dominant
What are Gain-of-function mutations?
- Change the gene product such that it gains a new and abnormal function.
- These mutations usually have dominant effects, expressed also in heterozygotes.
What are Loss-of-function mutations?
- gene product having less or no function.
- Phenotypes associated with such mutations are most often recessive.
What are the molecular events if there is Gain of function mutation?
- Pregnancy-induced hypertension
- Gain of function mutation in mineralocorticoid receptor gene
- Because of the mutation the receptor will be also activated by progesterone whose level increases 100-fold during pregnancy, causing salt retention, expansion of blood plasma volume and skyrocketing blood pressure.
Give an example of Gain of function mutations
- Gain of function mutations in fibroblast growth factor receptor 3 (FGFR3) gene cause achondropasia-t.
- The normal function of FGFR 3 is to slow down the formation of bone by inhibiting the proliferation of chondrocytes, the cells that produce cartilage.
- The mutation increases the activity of FGFR 3, severely limiting bone growth.
Describe Haploinsufficiency
- When 1 copy of an allele is not enough
- Special case of loss-of-function mutation
- reduced dosage of a normal gene product is not enough (=haploinsufficiency) for a normal phenotye, so it is expressed in heterozygotes (e.g. Marphan syndrome)
43
Give an example for haploinsufficiency
- Mutation in MC4R gene is the most frequent monogenetic cause for morbid obesity (BMI >40).
- 6% of extreme obese individuals has mutation in MC4R.
Describe Dominant negative mutation
- Special case of loss-of-function mutation
- Inhibits the function of normal allele
Give an example of Dominant negative mutation
- Dominant negative mutations in the Keratin 9 gene causes epidermolytic palmoplantar keratoderma
- All the mutations are in the highly conserved coil 1A of the rod domain, thought to be important for heterodimerisation.
By the fitness, mutations can be …
- (Most are apparently) neutral
- (few are) harmful – causing diseases
The apparently neutral mutations may also have functions
=> What are they?
- May influence the effect of environmental factors (gene-
environmental interaction) - May influence the effect of other variations (gene-gene interaction)
- May influence disease risk or other traits
The apparently neutral mutations may also have functions
=> What are they?
- May influence the effect of environmental factors (gene-
environmental interaction) - May influence the effect of other variations (gene-gene interaction)
- May influence disease risk or other traits
Some gene deficiencies can be beneficial
=> What are the 5 examples?
- CCR5∆32 – HIV resistance
- sickle cell anemia – malaria resistance
- G6PDH deficiency (favism)– malaria resistance
- FUT2 deficiency: norovirus resistance
- LPA deficiency lower risk of heart attacks and stroke
=> Most variations were acquired several thousand years ago by one individual and became widespread due to selective advantage
Classify mutations based on size
- Large scale
- Medium scale
=> Both of them are Cytogenetics (visible by M) - Small scale (not visible – only by molecular genetic methods)
Classification of mutations based on size
1. Describe large scale mutations
- Genome mutation = change of chromosome number
- Cytogenetics (visible by M)
Classification of mutations based on size
2. Describe medium scale mutations
Chromosome mutations = change of chromosome structure
Classification of mutations based on size
3. Describe medium scale mutations
- Affecting the length of DNA
- Deletion (single base or shorter-longer sequences)
- Insertion (single base or shorter-longer sequences - repetitive)
+) there are more insertions than deletions - No effect on the length of DNA
- nucleotide substitution, inversion
What is the percentage of Repetitive sequences (most of them are NOT in coding regions)?
46%
Repetitive sequences
1. What are the 2 types of Repetitive sequences?
- Tandem repeats
- Interspersed repeats (transposons)
Repetitive sequences
2. What are the 4 types of tandem repeats?
- Satellite DNA
- VNTR - Variable number of tandem repeats
- Minisatellite
- Microsatellite (STR=short tandem repeats)
Repetitive sequences
2A. Describe Satellite DNA
Satellite DNA is the main component of functional centromeres, and form the main structural constituent of heterochromatin.
Repetitive sequences
2B. Describe Minisatellite
- 7-100 bp
- E.g. Telomere
Repetitive sequences
2C. Describe Microsatellite
- 2- 6 bp
- Repeat number expansion => diseases (higher mutational rate)
Repetitive sequences
3. Describe interspersed repeats (transposons)
- SINEs (Short Interspersed Elements )
+) e.g. Alu: 10.6% of the genome! - LINEs (Long Interspersed Elements )
+) e.g. L1 - VNTR = variable number of tandem repeats: mini and microsatellite
Describe Repeat expansion disorders
- 3-12 bp
- The expansion of repeat length (i.e. the number of repeat units) across generations results in at least 50 known disorders.
- Dynamic mutation
Describe Deletion or insertion of nucleotide (a single or more)
- It is a frameshift mutation if number of nucleotide is not a multiple of three, and in-frame if number of nucleotide is a multiple of three
- Might be caused by replication slippage
Describe Deletion or insertion of nucleotide (a single or more)
- It is a frameshift mutation if number of nucleotide is not a multiple of three, and in-frame if number of nucleotide is a multiple of three
- Might be caused by replication slippage
Describe Deletion and nonsense mutation in Duchenne and Becker muscular dystrophy
The role of Gene duplication
- Provide important source of new gene
- Gene duplication is a special form of insertion
What is the result of Transposon insertion?
- Transposon insertion may result gene inversion
- Intrachromosomal recombination
- Inversion mutation due to intrachromosomal homologous recombination between mispaired copies of a repeat located within intron 22 and outside of the F8 gene.
Give the example of Transposon insertion
This mutation is responsible for 40% of Hemophilia A cases
- VIII. Blood clotting factor gene (F8)
- L1 repeat sequence (transposon)
What are the 2 types of Nucleotide substitutions?
What are the 3 types of Nucleotide substitutions in exons
- Silent mutation
- Missense mutation
- Nonsense mutation
Give an example of Missense mutation – sickle cell anemia
Give the Frequences of disease causing mutations
- Splicing 9.8%
- Deletion, 21.8%
- Insertion & duplication 6.8%
- Missense & Nonsense, 58.9%
What are 3 different meanings of polymorphism
– Phenotype polymorphism (normal, but different traits)
–Protein polymorphism (Immunoglobulins, ABO blood groups)
– Genetic (DNA) polymorphism (still in use in the meaning of apparently neutral variants, but see earlier)
Describe DNA variants
- Most are in non-coding sequences
- Density is highest in introns - Most are neutral
- Frequent variants (SNP and STR) are used as markers for personal identification, in population genetic studies and in linkage and gene association studies (see later)
- STRs are also used in prenatal diagnosis as markers
Chromosomal mutations (extreme) rarely can lead to ___
development of new species
