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Genomics > Epigenetics > Flashcards

Epigenetics Flashcards

1
Q

What is the heritability of epigenetic changes?

A

Still up for discussion

There is proof to show either side of the coin

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2
Q

What is epigenetics?

A

Broad definition

Includes any modification that changes how the DNA is used, switched on or off and changes in different tissues

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3
Q

What is the nature of epigenetics like?

A

Dynamic

Change during healthy development and ageing

Can be disturbed in certain diseases like cancer

Change due to environmental factors

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4
Q

Examples of environmental factors that affect epigenetic profiles

A

Drug exposure

Excercise

Medicine

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5
Q

What are the two main types of epigenetic changes?

A

Histone modification

DNA mehtylation

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6
Q

Mechanisms of histone modification

A

Acetylation

Methylation

Phosphorylation

Ubiquination

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7
Q

What does histone acetylation determine?

A

How strongly wrapped the DNA is bound around the histones

Adding an acetyl group = more expressed since the TF can get to the genes

Removing an acetyl group = less expressed since the TF can no longer access it

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8
Q

What does euchromatin represent?

A

A more loosely packed DNA, since it wraps around histone proteins less strongly

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9
Q

What does heterochromatin represent?

A

A more tightly packed DNA, since it wraps around proteins more strongly

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10
Q

What are enhancers?

A

Activate the transcription of a certain gene sequence

Can influence the expression of 100s of different genes along the chromosome

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11
Q

What is the difference between enhancers and promoters?

A

Enhancers are found on locations far away from where the DNA is transcribed

Promoters are normally found right next to the gene sequence

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12
Q

What is histone methylation?

A

Addition of methyl groups to the amino acids making up the histones

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13
Q

Are the effects of histone methylation always the same?

A

No

Depends on the amino acid they methylate

Methylation events that weaken chemical attractions between histone tails and DNA increase transcription

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14
Q

What sites on a histone protein does methylation take place?

A

Lysine

Arginine

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15
Q

Do histone modifications always cause the same changes?

A

No

Location and type of modification determines the effect on gene activation and repression

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16
Q

What is DNA methylation?

A

Methylation of CpG islands in the DNA

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17
Q

What are CpG regions?

A

Areas in the DNA where cytosine is found next to guanine

These are sites of methylation

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18
Q

Is the effect of methylation on gene expression always the same?

A

No

Depends on the location of methylation

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19
Q

Methylation in which location is associated with up-regulation of genes?

A

Gene body methylation

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20
Q

Methylation in which location is associated with down-regulation of genes?

A

Promoter methylation

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21
Q

Why does promoter methylation lead to down-regulation of genes?

A

Promoter region is bound by methyl groups

So the promoters cannot bind to the DNA sequences

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22
Q

Is methylation symmetrical?

A

Yes

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23
Q

What does the fact that methylation is symmetrical mean?

A

Methylation patterns are heritable from cell to cell following semi-conservative replication

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24
Q

Why have more studies been conducted on DNA methylation patterns compared to histone modifications?

A

Freezing samples destroys the histones but not the methylation patterns of the sample

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25
Q

What can we predict looking at the methylation patterns?

A

Ageing

Call type

Whether the individual is a smoker or not

26
Q

Why can we predict age by looking at methylation patterns?

A

Methylation patterns change in precise DNA segments

27
Q

Why can we predict cell type by looking at methylation patterns?

A

Each cell has distinct methylation patterns

Some are unique to the cell

28
Q

Why can we predict if a person is a smoker by lookng at the methylation patterns?

A

The epigenomic profule of a specific segment of DNA is particularly affected by smoking

29
Q

Why is looking at the histone modifications of a sample not practical?

A

Requires fresh samples

Less stable than DNA methylation

30
Q

Practicalities of DNA methylation

A

More stable

Can be performed on frozen DNA

31
Q

Factors that change methylation profiles of DNA

A

Environment

Ageing

Disease

32
Q

Environmental factors that change DA methylation profiles

A

Smoking

Excercise

Diet

Medication

33
Q

Describe the characteristic changes in DNA methylation profiles of cancer cells

A

Localised hypermethylation in promoters of tumour suppressor genes = suppression of tumour suppressor genes

Global hypomethylation leads to genomic instability and contributes to cell transformation

34
Q

Name 4 technologies used for investigating DNA methylation

A

Enzyme based methods

Methylation microarrays

Targeted sequencing techniques

Whole genome bisulfite sequencing

35
Q

How are enzyme based methods often used for investigating DNA methylation?

A

Crude information

Gives a good review of methylation

36
Q

Examples of enzyme based methods to look at DNA methylation

A

ELISA

Methylation specidic PCR

Methylation sensitive restriction enzymes

37
Q

Examples of methylation microarrays

A

MethyLight

38
Q

Explain how MethyLight works

A

Looks at one CpG at a time so has little coverage

But cost means it is used a lot in the clinic

39
Q

Examples of targeted sequencing techniques

A

Sanger bisulfite sequencing

MethyLight qPCR

Reduced representation bisulphite sequencing

40
Q

What promises to be the future of methylation analysis?

A

Nanopores

41
Q

What is the underlying mechanism in Bisulfite conversion?

A

Conversion of an epigenetic signature into a genetic signature

42
Q

What does Bisulfite conversion tell you?

A

The proportion of the DNA that is methylated vs the proportion that is not

No information of where the methylation takes place

43
Q

What happens if the bisulfite is added for too long?

A

Both the methylated and unmethylated cytosines will be deaminated into uracil

44
Q

How can we check that there hasn’t been too much bisulfite added to the mixture?

A

Check the cytosines not next to guanine

Make sure there have not been converted to thymine

45
Q

What technologies can be used to look at epigenetic modifications?

A

Microarrays

Sequencing

46
Q

Information obtained from microarrays?

A

Differentially methylated positions

Differentially methylated regions

Copy number variations

Epigenetic age estimation

Smoking prediction

47
Q

Advantages of sequencing

A

Greater coverage across the genome

Can identify novel gene variants and structural variations

Unbiased

48
Q

Disadvantages of sequencing

A

Expensive

Very complex analysis

49
Q

Advantages of microarrays

A

Cheap

Well validated analysis

Low amount of DNA

50
Q

Disadvnatages of microarrays

A

Limited to a certain number of known loci

Depend on prior sequence knowledge

Biased

51
Q

What is important to consider in epigenomic studies?

A

Confounders

52
Q

What are confounders?

A

Change the results through a separate mechanism different from what we are looking for

Provide false positive/negatives

53
Q

What is the problem with epigenomic studies?

A

A lot of factors can affect the genome

Designing a study can be very difficult

54
Q

What are the two types of confounders?

A

Technical

Biological

55
Q

Examples of technical confounders

A

DNA quality affected by storage technique

Bisulfite conversion efficiency

Batch effects - different lab technicians prepare the samples slightly differently and introduce errors

56
Q

Examples of biological confounders

A

Genetics - female X chromosomes are silences to prevent the effect of gender bias

Different cell types have different methylation profiles

Environmental exposures

Therapies - cancer therapies are known to alter methylation profiles

57
Q

Real life example of effect of confounders on results

A

Paper published that epigenetic changes were observed between older and younger patients

In reality, the epigenetic changes were caused by different cell populations in older populations

Older people = more monocytes

So the changes in epigenomic profiles were caused in reality by cellular heterogeneity

58
Q

Methods to minimise technical confounding

A

Rigorous quality control

Randomise samples

Normalisation

59
Q

Methods of reducing biological confounding

A

Important to select correct cell you want to use since cellular heterogeneity increases genetic heterogeneity

Match populations for gender, age, environmental exposures and therapy

60
Q

What is the most ideal study cohort?

A

Longitudinal analysis of epigenetic changes in monozygotic twins

Genomics (9 decks)

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