Epigenetics and Abnormal Gene Expression

Question 1

What is the central dogma of information flow in epigenetics?

Answer 1

DNA - loop back via replication 
I    
I    transcription
I
V 
RNA - loop back via replication - can ^ return to DNA via reverse transcription 
I
I    translation
I
V
protein

Question 2

What are the two structures of note found on the chromosome?

Answer 2

Centromere

Telomere

Question 3

What overlays chromosome structure that can be used for identifying twins, etc?

Answer 3

Epigenetic tags

Question 4

What does epigenetic gene silencing involve?

Answer 4

Multiple mechanisms,
DNA methylation
Histone modifications
Nucleosome remodelling

Question 5

What are epigenetics?

Answer 5

The study of:
• Heritable modifications of DNA that do not alter the primary sequence (e.g. me-C at CpG)
• Result: Altered gene expression

Question 6

What is DNA methylation chemically?

Answer 6

• Covalent modification of a methyl group to cytosine at position C5 to make 5-methylcytosine.
• Most genes have GC rich areas of DNA in their promoter regions - CpG islands.
• Methylation of the C residues within the CpG islands leads to gene silencing
• Little or no detectable DNA methylation in yeast and Drosophila

Question 7

Is DNA methylation heritable?

Answer 7

Yeah

Question 8

Provide a broad overview of the effects of DNA methylation?

Answer 8

• DNA methylation inhibits gene transcription
• Methylation prevents the binding of transcription factors to the promoter and inhibits transcription by converting chromatin from an open to a closed conformation
• Methyl CpG binding proteins contain a methyl binding domain that specifically recognizes methylated CpGs
• Recruits other proteins such as histone deacetylases which remove acetyl groups, favouring compact chromatin

Question 9

What diseases may be linked to defects in DNA methylation machinery?

Answer 9

X-linked syndromes with variable phenotypes

e.g. Rett Syndrome:
dominant X-linked, neurodegenerative disorder
affects 1:10,000-15,000 (females only)
Caused by a mutation in the gene encoding Methyl-CpG-binding protein 2 (MeCP2),
which in turn leads to loss of gene silencing at many loci.

Question 10

What is Prader-Willi syndrome?

Answer 10

– mental retardation

– obesity

Question 11

What is Angelman syndrome?

Answer 11

– mental retardation
– “happy puppet” syndrome
– jerky movements + inappropriate laughter

Question 12

How are Prader-Willi and Angelman syndromes related?

Answer 12

They are both chromosome 15 abnormalities, however AS is a maternal deficiency and PWS is a paternal deficiency
Both due to defects in imprinted genes: defective expression in brain tissue

Question 13

Compare heterochromatin and euchromatin

Answer 13

Heterochromatin
Highly condensed in interphase
Transcriptionally inactive
(contains few genes)
Replicates late in S phase

Euchromatin
Organized in 30nm fiber during interphase
Transcriptionally active
Replicates early in S phase

Question 14

Does DNA higher order influence gene expression?

Answer 14

Yeah

Question 15

What can DNA higher order influence?

Answer 15

Gene expression

Question 16

What is the position effect?

Answer 16

The spreading of heterochromatin
into euchromatic regions causes
cell to cell variability
in gene expression

Question 17

What is the spreading of heterochromatin into euchromatic regions causing
cell to cell variability
in gene expression called?

Answer 17

position effect

Question 18

What does the spreading of heterochromatin into euchromatic regions cause?

Answer 18

Cell to cell variability in gene expression

Question 19

At what stage does the ratio heterochromatin in euchromatin regions become stable?

Answer 19

Early in the developing embryo, heterochromatin forms and spreads into neighbouring euchromatin to different extends in different cells.
These expression states are stably inherited in the daughter cells

Question 20

Describe X-chromosome inactivation

Answer 20

• Discrepancy of 1 X-chromosome in males (XY) but 2 X-chromosomes in females (XX)
• Solution - Females need to silence one X-chromosome - X-chromosome inactivation (Mary Lyon, 1961)

• Mechanism of silencing is initiated by Xist
- X-inactive-specific-transcript ‘marks’ inactive X:
only expressed from inactive X-chromosome and codes for an RNA (~17kb in humans). No protein product and RNA remains in the nucleus. Followed by DNA methylation.

Question 21

When is DNA methylation reset?

Answer 21

DNA methylation completely reset upon fertilisation

Question 22

What are Barr bodies?

Answer 22

A small, densely staining structure in the cell nucleus of females, consisting of condensed, inactive X chromosome

Question 23

What unusual inactivation scenarios can occur in X chromosome inactivation?

Answer 23

• Only 1 X chromosome should remain active:
so in rare examples such as a male with Klinefelter’s syndrome (where the genotype is 47XXY), the number of Barr bodies would also be 1.

Question 24

What is the classic cat based example of X chromosome inactivation?

Answer 24

• Calico (tortoiseshell) cats are female
• Random X-chr inactivation manifested
in coat colour (The paternal or the maternal X-chromosome express either orange or black coat-colour gene; white is autosomal)

Question 25

Describe genomic imprinting

Answer 25

• ~200 imprinted genes on autosomes
• Imprinted genes only expressed from one allele
• Dependent on parental origin
• Imprinting resets on passage through germline
• Patterns reset in gametes
that escape wave of de-methylation just after fertilisation
• In sperm, imprint is “paternal”
• In eggs, imprint is “maternal”

Question 26

What is uniparental disomy

Answer 26

• Both copies of a chromosome are inherited from the same parent
• Individual is missing the chromosome from one of the parents
• Expression altered of imprinted genes on affected chromosome (non-imprinted genes are not affected)
• Result: chr 15, PWS/ AS
chr 11, Wilms’ tumour

Question 27

Go into detail on the angelman syndrome

Answer 27

• genetic disorder that affects the nervous system and causes severe physical and intellectual disability
• caused when the Angelman gene, known as UBE3A, is either absent or malfunctions
• In most cases of Angelman syndrome (about 70%),
the child’s maternal copy of the UBE3A gene is missing (deleted), which means there’s no active copy of the UBE3A gene in the child’s brain. In a small number of cases, Angelman syndrome occurs when a child inherits two copies of chromosome 15
from the father, rather than inheriting one from each parent.
This is known as (paternal) uniparental disomy.

Question 28

Go into detail on Praeder-Willi Syndrome

Answer 28

• rare genetic condition that causes a wide range of physical symptoms, learning difficulties and behavioural problems
• caused by a fault in a group of genes on chr15
• fault leads to a number of problems and is thought to affect the hypothalamus, which produces hormones and regulates growth and appetite.
• Most cases of Prader-Willi syndrome (about 70%) occur when a segment of
the paternal chromosome 15 is deleted genes which means there’s no active copy of chr 15 in the child’s brain. In another 25%, a person has two copies of chr 15 inherited from the mother. This is known as (maternal) uniparental disomy.

Question 29

What results in uniparental isodisomy or uniparental heterodisomy?

Answer 29

• Non-disjunction in meiosis II -> uniparental isodisomy

* Non-disjunction in meiosis I -> uniparental heterodisomy

Question 30

What are some diseases that are associated with genomic imprinting?

Answer 30

Beckwith–Wiedemann (BWS) syndrome
Wilms’ Tumour
Fragile X syndrome
Myotonic dystrophy (congenital) Prader–Willi syndrome Angelman syndrome