The Epigenome

Question 1

Define the Genome.

Answer 1

DNA sequence that is present in a single full set of chromosomes

Question 2

What is the First level of DNA packing?

Answer 2

nucleosomes

-histone proteins bound to DNA

Question 3

What is chromatin?

Answer 3

organisation of DNA in nucleosomes:

> Euchromatin: gene-rich, transcriptionally active, dispersed appearance, unique DNA sequences

> Heterochromatin: gene-poor, less transcriptionally active, condensed appearance, repetitive DNA sequences

Question 4

Describe the Packing Solution of Genome.

Answer 4

· Nucleosomes are wound up to form 30nm fibres

· Fibres are then 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 total of heritable changes in the genome that do not occur in the primary DNA sequence which affect gene expression

*epigenetic change results in a change in phenotype but not in genotype

Question 6

What are the Types of epigenetic mechanisms?

Answer 6

DNA methylation
Histone modification
X-inactivation
Genomic imprinting

Question 7

What is DNA methylation?

Answer 7

DNA methylation is the addition of methyl groups (-CH3) in the 5’ position of a cytosine

• doesn’t happen at every cytosine in DNA
• occurs in CpG dinucleotides in differentiated cells

Question 8

What is the Enzyme which catalyses DNA methylation?

Answer 8

DNA methyltransferase

-DNMT1, DNMT3a, DNMT3b

Question 9

What provides the methyl group for DNA methylation?

Answer 9

S-Adenosyl Methionine (SAM)

-becomes S-Adenosyl Homocysteine (SAH) due to loss of methyl group

Question 10

How does DNA methylation affect gene expression?

Answer 10

turns transcription off by preventing the binding of transcription factors

Question 11

What is DNA demethylation?

Answer 11

removal of the methyl group, converting the nucleotide back to cytosine via a number of intermediates (not directly back to cytosine):
>5-hydroxymethylcytosine
>5-formylcytosine
>5-carboxycytosine

Question 12

What is histone modification?

Answer 12

addition of chemical groups to histone proteins

Examples:

• acetylation
• methylation

Question 13

How are histone modifications named?

Answer 13

Modifications are named based on the histone it affects, the amino acid and the actual modification.

For example, a modification called H3K4Me3 means that it is a modification on Histone 3, the Lysine at position 4 and is tri-methylated.

Question 14

What are the enzymes that add modifications to histone tails called?

Answer 14

WRITERS

Histone acetyltransferase (HAT1)
Histone methyltransferase (EHMT1)

Question 15

What are the enzymes that remove modifications to histone tails called?

Answer 15

ERASERS

Histone Deacetylase (HDAC1)
Histone Demethylase (KDM1)

Question 16

Enzymes which bind to histone modifications and alter gene activity and protein production are known as…

Answer 16

READERS

Bromodomain and Extra-terminal (BET) proteins- BRD2

Chromodomain proteins -CBX1

Question 17

What are the Effects of histone modification?

Answer 17

Histone acetylation at Lysine residues relaxes chromatin structure, making it more accessible for transcription factors

Histone methylation is more complex and can repress or activate transcription depending on where it occurs

Histone modifications can occur concurrently and so their effects can interact or modify each other

Question 18

What is X-inactivation?

Answer 18

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

Question 19

What is the Importance of X inactivation?

Answer 19

ensures that every somatic cell in all humans has the same number of active copies of every gene (because Y chromosome in males has virtually no genes)

Question 20

What are the Steps of X inactivation?

Answer 20

· The Xist gene is transcribed as a long non-coding RNA (lncRNA) from the X-inactivation centre (Xic) and binds all over the X-chromosome to regulate gene expression

·Histone acetylation is removed and histone and DNA methylation occurs to inactivate that chromosome

·Inactive X-chromosome is heterochromatic and is referred to as Barr body

Question 21

How to prevent other X chromosome from inactivating?

Answer 21

·You don’t want both X chromosomes to be inactive and so one chromosome transcribes Tsix gene in the opposite direction from a reverse sequence long noncoding RNA and antagonises Xist RNA to keep one X active.

Question 22

What is genomic imprinting?

Answer 22

Genomic imprinting refers to selective expression of a gene depending on whether it was inherited from the male parent or the female parent.

Question 23

Where are imprinted genes found?

Answer 23

in clusters in autosomes

Question 24

What is imprinting mediated by?

Answer 24

imprinting control regions (ICRs), which silence genes near them using DNA methylation and histone methylation

• one copy is silenced by DNA methylation catalysed by DNMT3s and histone methylation leading to inactivation
• long noncoding RNAs (lncRNAs) are essential to the process (like X-inactivation)
• imprinting patterns are reset during gamete formation

Question 25

What are Pharmacoepigenetics?

Answer 25

studies the underlying epigenetic patterns that lead to variation in an individual’s response to medical treatment.

Question 26

What is the pharmacoepigenetics field split into?

Answer 26

Two areas:

• Epigenetic regulation of genes
• Epigenetic effect of drugs

Question 27

Describe epigenetics in cancer.

Answer 27

· Global DNA methylation is altered in tumour cells
>Hypermethylation of tumour suppressor genes (reducing gene expression)
>Hypomethylation of tumour activating genes (increasing gene expression and favouring cancer formation)

Question 28

Give some Epigenetic enzymes in tumour cells.

Answer 28

epigenetic enzymes are often mutated in tumour cells:

• DNMT3a and TET1/2
• Histone Acetyltransferases
• Histone Methyltransferases
• Histone Kinases
• Histone Readers (acetyl/methyl/phosphoryl)
• Histone Demethylases

Question 29

Give some Pharmacoepigenetic drugs in cancer treatment.

Answer 29

DNA Methyltransferase Inhibitors

> 5-Azacytidine (Vidaza)

> Treatment of Myelodysplastic syndrome

Histone Deacetylase Inhibitors

> Romidepsin (Istodax)

> Treatment of Cutaneous T-cell Lymphoma