The epigenome

Question 1

Genome

Answer 1

• The complete set of genetic material in a cell
• The DNA sequence that is present in a single full set of chromosomes

• Histone proteins and DNA form the first level of packing – the nucleosome

Question 2

Packing solution

Answer 2

Histones
Nucleosomes
Fibres and higher structures
Chromosomes are the most densely packed form of genomic DNA

Question 3

Epigenome

Answer 3

• The sum of all the (heritable) changes in the genome that do not occur in the primary DNA sequence and that affect gene expression
• An epigenetic change results in “A change in phenotype but not in genotype”
• The epigenome is central to the regulation of gene expression

Question 4

Epigenetic mechanism

Answer 4

• DNA Methylation
• Histone modification
• X-inactivation
• Genomic Imprinting

Question 5

DNA methylation

Answer 5

• DNA methylation in humans is the addition of a methyl group in the 5’ position of a Cytosine
• This is catalysed by DNA methyltransferase enzymes
• It requires S-Adenosyl Methionine to provide the methyl group
• In differentiated cells it occurs in CpG dinucleotides

Question 6

DNA methylation enzymes

Answer 6

DNMT1, DNMT3a and DNMT3b

Question 7

TET

Answer 7

Ten-Eleven translocation enzyme

Question 8

TDG

Answer 8

Thymine DNA glycosylase

Question 9

BER

Answer 9

Base excision repair

Question 10

2-OG

Answer 10

2-oxoglutarate

Question 11

DNA methylation and gene expression

Answer 11

• In general, DNA Methylation turns transcription off by preventing the binding of transcription factors
• DNA methylation patterns change during development and are an important mechanism for controlling gene expression

Question 12

Histone modifications

Answer 12

• This is the addition of chemical groups to the proteins that make up the nucleosome
• There are a large number of known histone modifications (>100) and many are of unknown function
• Large range of enzymes catalyse modification

Question 13

Common histone modifications

Answer 13

• Methylation
• Acetylation
• Phosphorylation
• Ubiquitination

Question 14

H3K4Me3

Answer 14

Histone 3, the Lysine (K) at position 4 is tri-methylated

Question 15

HAT1

Answer 15

Histone Acetyltransferase

Question 16

EEHMT1

Answer 16

Histone Methyltransferase

Question 17

HDAC1

Answer 17

Histone deacetylase

Question 18

KDM1

Answer 18

Histone demethylase

Question 19

Role of histone modifications

Answer 19

• Histone acetylation at Lysine residues relaxes the chromatin structure, by reducing positive charge on the histones, and makes it 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 will interact

Question 20

X-inactivation pt 1

Answer 20

• This is the inactivation of one of the two X chromosomes in every somatic cell in females
• This is needed as the Y chromosome has virtually no genes, so there is only one copy of each X chromosome gene in males (hemizygosity)
• X-inactivation ensures that every somatic cell in all humans has the same number of active copies of every gene

Question 21

X inactivation pt 2

Answer 21

The Xist gene is transcribed as a long noncoding RNA (lncRNA) from the X-inactivation centre (Xic) and binds all over the X-chromosome
• Histone acetylation removed and histone and DNA methylation occurs
• 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 22

Genomic imprinting

Answer 22

• Imprinting is the selective expression of genes related to the parental origin of the gene copy
• Every autosomal gene has one paternal and one maternal copy
• Imprinted genes tend to be found in clusters
• There are very few imprinted genes (~250)
• Imprinting is mediated by imprinting control regions (ICRs)
• One copy is silenced by DNA methylation catalysed by DNMT3a and histone methylation leading to inactivation
• LncRNAs are essential to the process
• Imprinting patterns are reset during gamete formation

Question 23

ADME

Answer 23

Absorption
Distribution
Metabolism
Excretion

Question 24

Enzymes related to mutated tumour cells

Answer 24

DNMT3A and TET1/2
	Histone Acetyltransferases
	Histone Methyltransferases
	Histone Kinases
	Histone Readers (acetyl/methyl/phosphoryl)
	Histone Demethylases

Question 25

Cancer and epigentics

Answer 25

Global DNA methylation is altered in tumour cells
Hypermethylation of tumour suppressor genes
Hypomethylation of tumour activating genes
Epigenetic enzymes are often mutated in tumour cells

Question 26

Pharmacoepigenetic drugs

Answer 26

•	DNA Methyl Transferase Inhibitors
	5-Azacytidine (Vidaza)
	Myelodysplastic syndrome
	Histone Deacetylase Inhibitors
	Romidepsin (Istodax)
	Cutaneous T-cell lymphoma
	Seven drugs FDA-approved so far