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COD Epigenetics Flashcards

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1
Q

What are epigenetic modifications?

A

Marks that can be added or removed from DNA

They control how and when genes are transcribed and are inherited when cells divide

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2
Q

What is epigenetics?

A

The study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence

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3
Q

What is the definition of DNA methylation? SIMPLE

A

DNA can be tagged with methyl groups

They are added to to some of its C residues

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4
Q

What is the definition of histone modification?

A

Tags can be added to histones that are closely associated with DNA

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5
Q

What are histones?

A

Basic proteins that associate with DNA in the nucleus and help condense it into chromatin

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6
Q

Describe the process of DNA methylation? MEDIUM

A

Chemical modification of DNA by the additon of a CH3 group to the number 5 carbon of the cytosine pyrimidine ring
This only occurs when cytosine is next to guanine

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7
Q

How is 5-methylcytosine produced?

A 
By the action of the DNA methyltransferases
These are:
DNMT1
DNMT3a
DNMT3b
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8
Q

What do the DNA methyltransferases catalyse?

A

The transfer of a methyl group from a donor to the carbon-5 position of cytosine

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9
Q

In vertebrates, all methylated cytosines are found in pairs of what?

A

CGs

And methylation is symmetric

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10
Q

Why are CG dinucleotides 5x less frequent than expected?

A

The mC has a tendency to mutate to T

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11
Q

What are CpG islands?

A

Regions with a high frequency of CpG sites
CG occurs at a normal frequency in these islands
0.5-2kb regions
Commonly located at 5’ end of many genes
Often overlap with promoter and 1st exon
56% of human genes have a CpG island

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12
Q

Are cytosines unmethylated or methylated in CpG islands?

A

Unmethylated

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13
Q

Describe the main mechanisms by which the methylation of DNA can prevent the description of genes
1) By changing the recognition sequence

A

The methyl group changes the recognition sequence
This prevents proteins binding
This attracts a different protein (binds a methylated DNA)

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14
Q

Describe the main mechanisms by which the methylation of DNA can prevent the description of genes
2) Recruiting protein complexes

A

Methyl binding domain proteins (MBDs) recruit protein complexes that modify histones
MBDs bind methylated promoter and recruits other proteins and the promoter is silenced

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15
Q

What is DNA methyltransferase 3L?

A

An accessory protein

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16
Q

Where does de novo methylation usually occur?

A 
In germline and early embryos
Can also occur in adults:
adult stem cells
certain tissues during aging
cancers
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17
Q

How does methylation occur? HARD

de novo

A

Unmethylated DNA becomes methylated via de novo DNA methylation. DNMT3a/b/L is used to do this
This becomes fully methylated DNA
DNA replication produces hemi methylated DNA
Maintenance methylation occurs with the help of DNMT1
DNMT1 is recruited to the replication fork by PCNA and UHRF1

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18
Q

What is passive DNA demethylation?

eg several divisions

A

Occurs over several cell divisons
There is a loss of 5mC during successive rounds of replication in the absence of function DNA methylation maintenance machinery

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19
Q

What is active DNA demethylation?

A

Enzymatic process that removes or modifies the methyl group from 5mC

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20
Q

What is 5hmC?

A

DNA pyrimidine nitrogen base derived from cytosine
The hydroxymethyl group on the cytosine can possibly switch on or off
It is the first oxidative product in the active demethylation of 5mC
Prevalent in embryonic stem cells and in the brain
Reduced levels of TET1 and subsequently 5mC cause impaired self renewal of stem cells

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21
Q

How does 5-methylcytosine become cytosine?

eg enzymes

A

By oxidation by TET enzymes

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22
Q

What are the core histones?
Describe them
eh h2a…
loose…

A

H2A,H2B,H3,H4
DNA is wrapped around histones
They have tails that protrude from the nucleosome
They can be modified
Eg methylated, phosphorylated, ubiquintilated
They can change the structure of the chromatin
Looser=euchromatin=active
Tighter=heterochromatin=silent
These modifications are also recognised by other proteins

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23
Q

Acetylation of lysines of histone H3 tails by WHAT is associated with gene expression/active chromatin?

A

Histone acteyl transferases (HATs)

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24
Q

Methylation of H3K4 on histone H3 tails by WHAT is associated with gene expression/active chromatin

A

HIstone methyltransferases (HMTs)

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25
Q

Absence of WHAT methylation is associated with gene expression

A

DNA

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26
Q

Removal of acetylation by WHAT is associated with gene silencing

A

Histone deacetylases (HDATs)

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27
Q

Methylation of H3K9 and H3K27 by WHAT is associated with gene silencing?

A

HIstone methyltransferases (HMTs)

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28
Q

Presence of DNA methylation is associated with more or less permanent gene silencing?

A

More permanent

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29
Q

During DNA replication, histones are recycled to form new what?

A

Nucleosomes

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30
Q

Can histone modifications be inherited through the cell cycle?
Describe model 1 (MTCs re-establish…)

A

After DNA replication, the methylated nucleosomes are distributed equally
to the 2 daughter strands
new MTCs (methyltransferase complex) re-establish the methylated domain

31
Q

Can histone modifications be inherited through the cell cycle?
Describe model 2 (Modified histones lost…)

A

AFter DNA replication, the modified histones are lost but the MTC complext is retained
at the replication fork
The MTC complex then methylated the new complex

32
Q

Describe a disease associated with mutations in ‘epi-regulators’.

A

Rett syndrome
Affected gene is MECP2
Reduced methyl-DNA binding due to mutation in MECP2
Mental retardation…loss of aquired speech
OR
Weaver syndrome
Affected gene is EZH2
Reduced H3k27me3 MTase activity due to mutations in EZH2
Pre and postnatal overgrowth, developmental delay

33
Q

What is dosage compensation?

A

Mammels use epigenetic mechanisms to inactivate one of the X chromosomes in female cells
The inactive X chromosome adopts a heterochromatic structure known as the Barr Body

34
Q

What is Xist?

A

X inactive specific transcript
Underpins Xic function, expressed from XIC
Non coding
Transcribed only from the inactive X chromosome elect
Xist RNA coats the inactive X chromosome territory
Necessary for X inactivation

35
Q

What is XIC?

A

The X inactivation centre
A cis-acting master switch locus that controls X inactivation
Inactivation starts at XIC (human)

36
Q

What is Tsix?

A

Non-coding RNA

Expressed antisense to XIst

37
Q

All X chromosomes express Xist at the what cell stages?

A

4-8

38
Q

What are the chromatin features on active x chromosomes Xa?

A

Histone tails acetylated
Histone H3 lysine 4 methylation on promoters
Variant histones H3.3 and H2Abb enriched
DNA methylation in gene bodies
Gene promoter depleted of DNA methylation

39
Q

What are the chromatin features on inactive x chromosomes Xi?

A 
Histone tails hypo-acetylated
Histone H3 lysine 4 methylation depleted
Polycombe histone modifications enriched
DNA methylation of gene promoters
DNA hypo-methylation in gene bodies
40
Q

What is no longer required when inactivation is established? (chromosomes)

A

Xist

41
Q

Describe cloning in relation to X chromosome activation

A

Cloning reactivates both X chromosomes
Inactivation recurs randomly
This can produce a diff coat colour for a cat eg
Even though mum and child is genetically identical

42
Q

What are the features of an X chromosome?

A

> 150m base pairs
1400 genes
p and q

43
Q

What are the features of a Y chromosome?

A

<60m base pairs
<200 genes
p and q and SRY = testes determining factor

44
Q

What is a sex linked disorder?

A

Where the abnormal gene is on either the x or y chromosome

45
Q

Describe X linked recessive disorders

eg if mutant gene is passed from female parents

A

Recessive mutation in one of the genes on the X
If mutant gene is passed from the female parent:
50% of male children will have the disease
50% of female children will be carriers
If mutant gene is passed from male parent:
No male children will have disease
All females will be carriers

46
Q

Main distinguishing features of X recessive

A

Parents will usually be phenotypically normal
Affected individuals usually male
No male to male transmission
Some female can be variably affected

47
Q

What is Haemophilia A

A

X linked recessive
5 in 100,000 male births
Genetic deficiency of blood clotting factor VIII
Joint and muscle haemorrhages, easy bruising

48
Q

What is X linked Hypohidrotic ectodermal dysplasia

A

Occurs in 1 in 100,000
X linked in males and females
Mutation in ectodysplasin-A (EDA)
Defect in hair, teeth and sweat glands

49
Q

Describe X linked dominant disorders

eg if mutant gene is passed from female parents

A

Dominant mutation of on of the X chromosomes
If mutant gene is passed from female, 50% all children will have the disease
If mutant gene is passed from male, no male children will have disease, all females affected

50
Q

Main distinguishing features of X dominant

A

One parent usually affected
Affected individuals can be male or female
No male to male transmission
Females can be variably affected (X inactivation)

51
Q

What is Rett syndrome?

A

X linked dominant
5 in 100,000
Usually affects females
Mutations in the methyl-CpG-binding-protein-2(MECP2)
Many cases are sporadic
Normal development and symptoms appear 7-18 months after
Autism,dementia,ataxia,loss of speech,seizures

52
Q

True or false?
Females with a recessive x linked condition can manifest some symptoms
AND
Females with a dominant x linked condition can be phenotypically normal

A

True

53
Q

Where the phenotype depends on a circulating product, there is an averaging effect between the normal and abnormal cells
Female carriers can have an intermediate phenotype but are usually clinically unaffected and biologically normal
Give an example

A

Haemophillia A

54
Q

Where the phenotype is a localised property of individual cells, female carriers can show patches of normal and abnormal tissue
Give an example

A

Hypohidrotic ectodermal dysplasia

DMD

55
Q

What is skewed x inactivation?

A

Caused by primary or secondary nonrandom x inactivation
Mutant x can become inactivated which would give a normal phenotype or the normal x can become inactivated with would give a diseased phenotype

56
Q

What is a Benign ovarian teratoma?

A 
A germ cell tumour
Rare
Teratoma consists of tissues derived from all 3 germ layers
Can have hair,skin,teeth
Most are benign
And most have 2 materinal genomes
57
Q

What is a Hydatidiform mole?

A 
A gestational trophoblastic disorder
Rare
Affects about 1 in 1200 pregnant women
Disorganised mass of placental tissue without a fetus
Most molar pregnancies are benign
Most have 2 paternal genomes
58
Q

How do you make a uniparental mouse embryo?

A 
Begin with a zygote
Remove the male or female pronucleus
In this case remove the male pronucleus
Add female pronucleus
Gynogenetic (GG)
It has 2 female derived genomes
59
Q 
Do the following have 2 paternal or maternal genomes?
Benign ovarian teratoma
Hydatidiform mole
Parthenogenetic embryo
Gynogenetic embryo
Androgenetic embryo
A 
Maternal
Paternal
Maternal
Maternal
Paternal
60
Q

What does it mean when we say the overian teratoma has 2 maternal genomes?

A

There is a loss of expression of normally paternally expressed genes
There is a gain in expression of normally maternally expressed genes

61
Q

True or false?
Genomic imprinting is an epigenetic process unique to mammals and some flowering plants and explains why mammals cannot develop parthogenetically

A

True

62
Q

Genomic imprinting is initiated by WHAT in germline

A

DNA methylation

One gamete aquires DNA methylation mark and the other does not

63
Q

Is DNA methylation maintained after fertilisation and cell division?

A

Yes

64
Q

Describe imprinted domains

A

Contain maternally and paternally expressed genes
Contain germline aquired DNA methylation ‘imprint’
DNA methylation on one parallel allele
DMR (differentially methylated region)

65
Q

Describe human chromosome 11p15

A

Contains several imprinted genes
Some are only expressed from maternal allele or paternal allele
Some are non coding RNAs
These are H19 (maternal) and LIT1 (paternal)

66
Q

What are DMRs
eg in 11p15
give examples

A

Differentially methylated regions
Human chromosome 11p15 contains 2 DMRs
H19DMR is methylated in sperm
Controls imprinted expression of IGF2 and H19
KvDMR1 is methylated in oocytes
KvDMR1 controls imprinted expression of CDKN1C and several additional maternally expressed genes

67
Q

What is IGF2?

A

Paternally expressed gene encodes Insulin- like growth factor 2
IGF2 promotes cell division and growth

68
Q

What is CDKN1C?

A

Maternally expressed gene
Encodes cyclin dependent kinase inhibitor 1c
It is a cell cycle inhibitor
Inhibits cell division and growth

69
Q

Genetic/epigenetic alterations at human chromosome 11p15 are associated with genetic imprinting disorders
Name 2

A

Beckwith Weidemann syndrome BWS

Silver russell syndrome SRS

70
Q

Describe Beckwith Weidemann syndrome BWS

A 
Fetal overgrowth syndrome
Affects 1 in 13,700
Babies in the 95th percentile at birth
Macroglossia (large tongue)
Cleft palate
Neonatal hypoglycaemia
Large placenta
Predisposition to Wilms' tumour
Some BWS patients have paternal disomy of human chr. 11p15 so 2 paternal copies
2 X IGF2 (too much)
0 X CDKN1C (not enough)
71
Q

The most common epigenetic alteration for BWS is loss of DNA methylation at KvDMR1
What does this mean?

A

At LIT1, there is a loss of DNA methylation
DNA sequence is not mutated
This is associated with a loss of CDKN1C

72
Q

Describe Silver russell syndrome SRS

A 
A fetal growth restriction disorder
Affects 1 in 100,000
Low birth weight - below 5th percentile
Poor postnatal growth
Classic facial phenotype
Assymmetry
Night sweats
Lack of subcutaneous fat
Some SRS patients have maternal disomy of human chr. 11p15
2 maternal copies
2 X CDKN1C
0 X IGF2
73
Q

What are epidrugs?

A

Drugs that target epigenetic marks
HDACs (Histone deactylases) remove acetyl groups from chromatin
DNA methylation inhibitors remove DNA methylation
Epigenetic diseases may be reversed using epidrugs

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