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COD Epigenetics Flashcards

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
Absence of WHAT methylation is associated with gene expression
DNA
26
Removal of acetylation by WHAT is associated with gene silencing
Histone deacetylases (HDATs)
27
Methylation of H3K9 and H3K27 by WHAT is associated with gene silencing?
HIstone methyltransferases (HMTs)
28
Presence of DNA methylation is associated with more or less permanent gene silencing?
More permanent
29
During DNA replication, histones are recycled to form new what?
Nucleosomes
30
Can histone modifications be inherited through the cell cycle? Describe model 1 (MTCs re-establish...)
After DNA replication, the methylated nucleosomes are distributed equally to the 2 daughter strands new MTCs (methyltransferase complex) re-establish the methylated domain
31
Can histone modifications be inherited through the cell cycle? Describe model 2 (Modified histones lost...)
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
Describe a disease associated with mutations in 'epi-regulators'.
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
What is dosage compensation?
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
What is Xist?
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
What is XIC?
The X inactivation centre A cis-acting master switch locus that controls X inactivation Inactivation starts at XIC (human)
36
What is Tsix?
Non-coding RNA | Expressed antisense to XIst
37
All X chromosomes express Xist at the what cell stages?
4-8
38
What are the chromatin features on active x chromosomes Xa?
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
What are the chromatin features on inactive x chromosomes Xi?
``` 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
What is no longer required when inactivation is established? (chromosomes)
Xist
41
Describe cloning in relation to X chromosome activation
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
What are the features of an X chromosome?
>150m base pairs >1400 genes p and q
43
What are the features of a Y chromosome?
<60m base pairs <200 genes p and q and SRY = testes determining factor
44
What is a sex linked disorder?
Where the abnormal gene is on either the x or y chromosome
45
Describe X linked recessive disorders | eg if mutant gene is passed from female parents
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
Main distinguishing features of X recessive
Parents will usually be phenotypically normal Affected individuals usually male No male to male transmission Some female can be variably affected
47
What is Haemophilia A
X linked recessive 5 in 100,000 male births Genetic deficiency of blood clotting factor VIII Joint and muscle haemorrhages, easy bruising
48
What is X linked Hypohidrotic ectodermal dysplasia
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
Describe X linked dominant disorders | eg if mutant gene is passed from female parents
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
Main distinguishing features of X dominant
One parent usually affected Affected individuals can be male or female No male to male transmission Females can be variably affected (X inactivation)
51
What is Rett syndrome?
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
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
True
53
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
Haemophillia A
54
Where the phenotype is a localised property of individual cells, female carriers can show patches of normal and abnormal tissue Give an example
Hypohidrotic ectodermal dysplasia | DMD
55
What is skewed x inactivation?
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
What is a Benign ovarian teratoma?
``` 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
What is a Hydatidiform mole?
``` 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
How do you make a uniparental mouse embryo?
``` 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
``` Do the following have 2 paternal or maternal genomes? Benign ovarian teratoma Hydatidiform mole Parthenogenetic embryo Gynogenetic embryo Androgenetic embryo ```
``` Maternal Paternal Maternal Maternal Paternal ```
60
What does it mean when we say the overian teratoma has 2 maternal genomes?
There is a loss of expression of normally paternally expressed genes There is a gain in expression of normally maternally expressed genes
61
True or false? Genomic imprinting is an epigenetic process unique to mammals and some flowering plants and explains why mammals cannot develop parthogenetically
True
62
Genomic imprinting is initiated by WHAT in germline
DNA methylation | One gamete aquires DNA methylation mark and the other does not
63
Is DNA methylation maintained after fertilisation and cell division?
Yes
64
Describe imprinted domains
Contain maternally and paternally expressed genes Contain germline aquired DNA methylation 'imprint' DNA methylation on one parallel allele DMR (differentially methylated region)
65
Describe human chromosome 11p15
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
What are DMRs eg in 11p15 give examples
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
What is IGF2?
Paternally expressed gene encodes Insulin- like growth factor 2 IGF2 promotes cell division and growth
68
What is CDKN1C?
Maternally expressed gene Encodes cyclin dependent kinase inhibitor 1c It is a cell cycle inhibitor Inhibits cell division and growth
69
Genetic/epigenetic alterations at human chromosome 11p15 are associated with genetic imprinting disorders Name 2
Beckwith Weidemann syndrome BWS | Silver russell syndrome SRS
70
Describe Beckwith Weidemann syndrome BWS
``` 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
The most common epigenetic alteration for BWS is loss of DNA methylation at KvDMR1 What does this mean?
At LIT1, there is a loss of DNA methylation DNA sequence is not mutated This is associated with a loss of CDKN1C
72
Describe Silver russell syndrome SRS
``` 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
What are epidrugs?
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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