The Epigenome

Question 1

What is the genome?

Answer 1

The complete set of genetic material in a cell

Question 2

How is the genome organised?

Answer 2

It exists in a cell as an organised structure made up of a number of macromolecules with DNA as the primary building block. Histones and other proteins provide a support around which the DNA is wound. These structures are then organised in 3D to form fibres and ultimately chromosomes

Question 3

What is a nucleosome?

Answer 3

Histone proteins and DNA that forms the first level of packaging

Question 4

How is DNA packaged?

Answer 4

• Nucleosomes are wound to form 30nm fibres
• Fibres are wound up further with scaffold proteins to generate higher-order structures
• Chromosomes are the most densely packed form of genomic DNA

Question 5

What is the epigenome?

Answer 5

The sum of all the heritable changes in the genome that do not occur in the primary DNA sequence and that effect gene expression.

Question 6

What is an epigenetic change?

Answer 6

A change in phenotype but not in genotype

Question 7

What are the epigenetic mechanisms?

Answer 7

DNA methylation
Histone modification
X-inactivation
Genomic imprinting

Question 8

What is DNA methylation?

Answer 8

It is the addition of a methyl group in the 5’ position of a cytosine.

Question 9

What catalyses DNA methylation?

Answer 9

DNA methyltransferase enzymes

Question 10

What are the DNA methyltransferase enzymes?

Answer 10

DNMT1, DNMT3a and DNMT3b

Question 11

What provides the methyl group in DNA methylation?

Answer 11

S-Adenosyl Methionine

Question 12

How does DNA methylation occur in differentiated cells?

Answer 12

It occurs in CpG dinucleotides

Question 13

How is DNA demethylated?

Answer 13

Through a series of steps:
1. 5-methylcytosine is converted via TET into 5-hydroxymethylcytosine as there is an addition of an OH onto the 5th carbon.

2. Then TET converts this into 5-formylcytosine (an aldehyde).
3. Then TET converts this into 5- carboxycytosine as an COOH group is added.
4. TDG and BER occur to convert 5-carboxycytosine, 5-formylcytosine or 5-hydroxycytosine back into cytosine through passive demethylation.

Question 14

What is TET?

Answer 14

It is Ten-Eleven Translocation enzyme

Question 15

What is TDG?

Answer 15

Thymidine DNA glycosylase

Question 16

What is BER?

Answer 16

Base Excision Repair

Question 17

When does passive demethylation occur?

Answer 17

It occurs during replication

Question 18

What is the importance of DNA Methylation?

Answer 18

• Turns off transcription by preventing binding of the transcription factors.
• Patterns change during development and are an important mechanism for controlling gene expression

Question 19

What is histone modification?

Answer 19

• The addition of chemical groups to the proteins that make up the nucleosome.

Question 20

How many histone modifications are there and what is there function?

Answer 20

About 100 modifications and many are of unknown functino

Question 21

What are the common histone modifications?

Answer 21

Acetylation and Methylation

Question 22

How are histone modifications named?

Answer 22

Based on the histone, the amino acid and the actual modification. For example, H3K4Me3 means on histone 3, the lysine at position 4 and it is tri-methylated

Question 23

What are histone writers? Give examples

Answer 23

Enzymes that add histone modifications. For example - Histone Acetyltransferase - HAT1
- Histone Methyltransferase - EHMT1

Question 24

What are histone erasers? Give examples

Answer 24

Enzymes that remove histone modifications.
For example:
- Histone deactylase HDAC1
- Histone demethylase KDM1

Question 25

What are histone readers? Give examples

Answer 25

Proteins that bind to the histone modification and alter gene activity and protein production. For example: - Bromodomain and extra-terminal (BET) proteins - BRD2 - Chromodomain proteins - CBX1

Question 26

Function of histone acetylation at lysine

Answer 26

At lysine residues, it relaxes the chromatin structure and makes it accessible for transcription factors

Question 27

Function of histone methylation

Answer 27

More complex than acetylation. Can repress or activate transcription depending on where it occurs

Question 28

What does the concurrence of histone modifications mean?

Answer 28

They can interact or modify each other

Question 29

What is X-inactivation?

Answer 29

Inactivation of one of the two X chromosomes in every somatic cell in females

Question 30

Why is X-inactivation required?

Answer 30

This is needed as the Y chromosome has virtually no genes, so there is only one copy of each X chromosome gene in males but in females, it is needed to make sure there is the same number of active copies of every gene in each somatic cell.

Question 31

How does X-inactivation occur?

Answer 31

- The Xist gene is transcribed as a long non-coding RNA (IncRNA) from the X-inactivation centre (Xic) and binds all over the X-chromosome. - Histone acetylation removed and histone and DNA methylation occurs - The inactive X-chromosome is heterochromatic - Barr body. - Tsix is derived by transcription in the opposite direction and antagonises Xist RNA to keep one X active.

Question 32

Give an example of an animal that has undergone X-inactivation

Answer 32

All tortiseshell cats are female. This is because they have one X with an active orange fur allele and one X with an active black fur allele. Random X-inactivation results in patches of orange and black fur.

Question 33

What is genomic imprinting?

Answer 33

Imprinting is the selective expression of genes related to the parental origin of the gene copy.

Question 34

How are imprinted genes found together?

Answer 34

In clusters.

Question 35

How many imprinted genes are there?

Answer 35

Very few imprinted genes - approximately 250

Question 36

What mediates gene imprinting?

Answer 36

The imprinting control regions (ICRs)

Question 37

How is one gene silenced in imprinting?

Answer 37

One copy is silenced by DNA methylation catalysed by DMNT3a and histone methylation leading to inactivation. LncRNAs are essential to the process.

Question 38

When is imprinting patterns reset?

Answer 38

They are reset during gamete formation

Question 39

Why is pharmacoepigenetics studied?

Answer 39

It is known to cause epigenetic regulation of genes or epigenetic effects of drugs.

Question 40

Why is it important to study the epigentic regulation of genes?

Answer 40

Information can be used to increase the efficacy of drug treatment

Question 41

Why is it important to study the epigenetic effects of drugs?

Answer 41

New paradigms for the drug treatment

Question 42

How is global methylation effected in cancer?

Answer 42

Known that global DNA methylation is altered in tumour cells. This causes: - Hypermethylation of tumour suppressor genes - Hypomethylation of tumour activating genes

Question 43

Which enzymes are affected in tumour cells

Answer 43

- DNMT3A and TET1/2 - Histone Acetyltransferases - Histone Methyltransferases - Histone Kinases - Histone Readers - Histone Demethylases These are often mutated in tumour cells

Question 44

What is an example of a pharmacoepigenetic drug?

Answer 44

DNA methyl transferase inhibitors - 5-Azacytidine (Vidaza) - Myelodysplastic syndrome - Histone deactylase inhibitors - Romidepsin (Istodax) - Cutaneous T-cell lymphoma