Human Genetic Variability

Question 1

Are all proteins found in the mitochondria all encoded by the mitochondrial or nuclear genome? Which genome is more compact?

Answer 1

Both- important thing to note is that mitochondrial genome is highly compact whereas nuclear genome is not

Question 2

The mitochondrial genome is a 16.6 double-stranded circular genome. How do the contents of each strand differ from each other?

Answer 2

The heavy strand (H strand) is G-rich whilst the light strand (L strand) is C-rich

Question 3

What is generated from a small region of the H strand?

Answer 3

7S DNA that forms a displacement loop that contains a control region of the genome

Question 4

How is mRNA made from the mitochondrial genome?

Answer 4

There are two origins of replication (one on each strand). Transcribed as two long precursor transcripts from two promoters then cleaved to produce mature mRNA

Question 5

How many genes are transcribed from the mitochondrial genome?

Answer 5

37- 28 on the H strand and 9 on the L strand
Only 13 of these are proteins, the rest are noncoding RNAs
Also all these genes lack introns and many overlap/ are contiguous

Question 6

How can it be evidenced that mitochondrial DNA is maternally inherited?

Answer 6

By using polymorphic markers e.g RFLPs

Question 7

What is meant by heteroplasmy?

Answer 7

This is what happens due to the cell having multiple mitochondria. This means that we have several copies of mtDNA and so the cell contains a mixture of genetically different mitochondria

Question 8

A new mutation in mtDNA will only affect the organelle in which it originated. Individuals with mitochondrial diseases are always what? What does the severity of the disease depend on?

Answer 8

Heteroplasmic. Mitochondrial mutations are lethal in the absence of normal mitochondriain the cell and so the severity depends on the proportions of mutated mitchondria compared to normal

Question 9

What do mitochondrial mutations affect and how are they characterised?

Answer 9

The ATP-generating capacity of the mitochondria and are characterised by defects in nerve and muscle function, blindness, deafness and stroke

Question 10

What sort of RNA in the mitochondria and mitochondrial diseases associated with?

Answer 10

mutations in the tRNA even though tRNA does not account for much of the genome

Question 11

What is the threshold effect? Use the mitochondrial disease MERFF as an example to help you explain.

Answer 11

It is when a certain % of the mitochondria are defective. E.g 80-90% defective mitochondria causes symptotms of MERFF

Question 12

What is MERFF?

Answer 12

Disease caused by a mutation in tRNA which affects all proteins encoded by the mtDNA in all cells in which the mutation is found. It is lethal in the absence of normal cells and causes hearing loss, seizures, fatigue, dementia, tremors and jerkiness

Question 13

Explain what physical and genetic bottlenecks are and how this affects transmission of mitochondrial DNA (in normal cells/eggs).

Answer 13

Eggs contain many mtDNAs. The individual that develops from this egg will have a reduced number of mitochondria per cell in the developing germ cells. This is due to a physical bottleneck where daughter cells only receive a small subset of the mitochondria of the parents cell. It is also due to a genetic bottleneck where not all mitochondria multiply efficiently

Question 14

Knowing that bottlenecks can affect mtDNA transmission between generations, how may this affect transmission of mutations in mtDNA to offspring?

Answer 14

May result in a very skewed ratio of mutant to normal mitochondrial DNAs in the daughter cells. This means future offspring will have very differing disease severity from their mother and siblings- this means this can become a very large percentage of total mitochondria in future generations

Question 15

When considering mutational processes that lead to genetic variation, is it germline or somatic processes that are relevant? What other factor is relevant?

Answer 15

Germline

Evolutionary timescales are also important

Question 16

When was the 1000 genome project initiated? How many people did it include? What alleles were looked at?

Answer 16

2008. Sequenced 2500 people from around the world using Next-generation sequencing to characterise variation between individuals. Interested in allele frequencies above 1% or of around 0.1% in coding regions

Question 17

What are DNA variants and how do they differ from polymorphisms?

Answer 17

DNA variants are mutations that result in alternative forms of DNA. If this becomes common (over 1% of pop have it), it is called a polymorphism. If the variant is as low as 0.1% in its frequency, it is called a rare variant

Question 18

What sort of genetic variation is the most common, occurring at 1 in 10^8 of our nucleotides mutating per generation?

Answer 18

SNPs- although it is the most common it still has an overall low mutation rate. This low mutation rate means these are stable over evolutionary time. It also means we have 60 de novo mutations that are not present in our parents

Question 19

In general, if any two genomes were compared, how often would you find an SNP? Where are these located?

Answer 19

Every 1000 nucleotides. These fall outside of critical genes and regulatory regions- but 10% of SNPs affect restriction endonuclease recognition sites

Question 20

Is the pattern of SNP variation in human genome random? What supports this?

Answer 20

No it is non-random. There are mutagenic and repair mechanisms which drive the variation.
E.g. Frequency of mutation at CG dinucleotides is higher than at other inucleotides because deamination of methyl CpG sequences results in C to T transitions and this is not efficiently recognised and repaired

Question 21

SNPs are stable over evolutionary time, If two individuals have the same variant, what can we assume?

Answer 21

They shared a common ancestor

Question 22

Why is it helpful if SNPs are binary (have two forms)?

Answer 22

This can help in elucidating ancestral state compared to derived states of species and help analyse the direction of change

Question 23

Is base substitution rate higher or lower in mitchondrial DNA compared to nuclear? Why?

Answer 23

Much higher (10X)- especially in ‘control regions’. Due to high levels of mutagenic oxygen free radicals that are byproducts of oxidative phosphorylation. Also, mtDNA has a higher turnover rate and is not packaged in protective chromatin- the single-stranded DNA in the D-loop is especially vulnerable (control region)

Question 24

What are indels?

Answer 24

Insertion/deletion variation of up to 50 nt. Frequency of this happening is 1/10th of single nucleotide substitutions

Question 25

What are copy number variations (CNVs)?

Answer 25

Just larger insertions/deletions of 100 nt to megabases, happen less often than indels but affect many nucleotides in one go

Question 26

Some insertions of LINE and SINE elements are polymorphic. How?

Answer 26

Once it is inserted into a particular sequence, it almost never leaves, so the polymorphism is the presence or absence of it so ancestral state is ‘absent’. This means if two individuals share an element in the same place it is almost always identity by descent

Question 27

Transposition can cause gene disruption which causes genetic disease. Name three.

Answer 27

Haemophilia A
Duchenne muscilar dystrophy
Cystic fibrosis

Question 28

Alu recombination plays a significant role in disease and what else?

Answer 28

Evolution

Question 29

Tandem repeats are highly polymorphic with variable numbers of repeats in the arrays of microsatellites, minisatellites and satellites. What is meant that these lead to multiallelic loci?

Answer 29

Have a high underlying mutation rate so can lead to many forms in contrast to SNPs which are binary

Question 30

If two individuals have the same multiallelic poymorphism (same number of repeats) of a tandem repeat, what is assumed about their ancestral state?

Answer 30

That it is not due to a common ancestor but rather a result of convergent evolution

Question 31

What are microsatellite polymorphisms also known as? What are they useful in/for?

Answer 31

Short tandem repeat polymorphisms (STRPs). They are highly polymorphic and so used in linkage analysis (paternal analysis/ forensic etc.)

Question 32

What causes the high mutation rate in microsatellites?

Answer 32

Slippage which leads to an increase or decrease in one repeat unit. This is sometimes corrected by the mismatch repair system. Defects in this system can lead to increased mutation rates (as found in some cancers)

Question 33

What is the correlation between mutation rate and array length?

Answer 33

Positive correlation

Question 34

What is the age effect on mutation rates and which gender is most affected by this?

Answer 34

In males, age is positively correlated with mutation rate due to the number of cell divisions increasing to make sperm. This is not the same case in females as all eggs are made before birth

Question 35

Minisatellites are also highly polymorphic. What is the mechanism driving this variation?

Answer 35

Recombination- unequal crossing over of sister chromatid regions. There is bias towards gain of units rather than losses. Satellite DNA also mutates through recombination mechanisms