The Epigenome

Question 1

Define what is meant by the 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

Question 2

What is meant by the Nucleosome?

Answer 2

The Nucleosome is the Histone proteins and DNA that form the first level of packing

Question 3

What is the packing solution?

Answer 3

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

Question 4

What’s are the two types of Chromatin?

Answer 4

Euchromatin and Hetero Chromatin

Question 5

What is Euchromatin?

Answer 5

• Gene rich
• Transcriptionally active
• Dispersed appearance
• Unique DNA sequences

Question 6

What is Hetero chromatin?

Answer 6

• Gene poor
• Less Transcriptionally active
• Condensed Appearance
• Repetitive DNA sequences

Question 7

What is meant by the Epigenome?

Answer 7

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

Question 8

What does an Epigenetic change result in?

Answer 8

A Change in the phenotype but not in the genotype

Question 9

Give an overview of the Epigenome

Answer 9

• The Epigenome is central to the regulation of gene expression
• Gene expression is regulated by DNA methylation and Histone modifications
• X activation and imprinting are important Epigenetic mechanisms for controlling expression from groups of genes

Question 10

What are Epigenetics used for?

Answer 10

Used to identify novel drug targets

Question 11

What are some epigenetic mechanisms?

Answer 11

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

Question 12

Describe what DNA methylation is

Answer 12

• In humans, it is the addition of a methyl group in the 5’ position of a cytosine
• The reaction is catalysed by the DNA methyltransferase enzymes
• Requires an S-Adenosyl Methionine to provide the methyl group
• Occurs in the CpG dinucleotides in differentiated cells

Question 13

How is DNA Methylation linked to gene expression?

Answer 13

• DNA methylation turns transcription off by preventing the binding of transcription factors
• DNA methylation pattern changes during development and are an important mechanism for controlling gene expression

Question 14

What is Histone Modification?

Answer 14

• The addition of chemical groups to the proteins that make up the Nucleosome
• There are large numbers of known Histone modifications (>100) but many of them are unknown functions
• There are a wide range of enzymes that can catalyse modification’s

Question 15

What are some common modifications?

Answer 15

• Methylation
• Acetylation
• Phosphorylation
• Ubiquitination

Question 16

What happens when amino acids are modified?

Answer 16

• Amino acids can be modified and can have anywhere between 1-4 groups added
• This gives a large number of modifications
• Others are known but poorly understood

Question 17

What are Histone modifications names based on?

Answer 17

Based on 3 different factors:
- The Histone
- The amino acid
- The Actual modification

Question 18

What are the 3 types of Histone modifiers?

Answer 18

• Writers
• Erasers
• Readers

Question 19

Give some examples of “writer” Histone modifiers

Answer 19

• Histone Acetyltransferase - HAT1
• Histone Methyltransferase - EHMT1

Question 20

Give some examples of “Erasers” Histone modifiers

Answer 20

• Histone Deacetylase: HDAC1
• Histone Demethylase: KDM1

Question 21

Give some examples of “Reader” Histone modifiers

Answer 21

• Bromodomain and extra-terminal (BET) proteins: BRD2
• Chromodomain proteins: CBX1

Question 22

What are the roles of Histone modifications?

Answer 22

• Histone acetylation at Lysone 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 23

What is X-Inactivation?

Answer 23

• The inactivation of one of the 2 X chromosomes in every somatic cell in females
• This is needed as the Y chromosome has virtually no genes, so there is only one group of each chromosome gene in males (Hemizygosity)

Question 24

What does X Inactivation ensure?

Answer 24

Ensures that every somatic cell in all humans has the same number of active copies of every gene

Question 25

Describe how X inactivation works (PART 1)

Answer 25

- 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

Question 26

Describe how X inactivation works (PART 2)

Answer 26

- 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 27

Give an example of X inactivation

Answer 27

- All tortoiseshell cats are female - Tortoiseshell cats have one X with an orange fur allele and one X with a black fur allele - Random X inactivation results in patches of orange and black fur

Question 28

What is Genomic Imprinting?

Answer 28

- It is the selective expression of genes related to the paternal origin of the gene copy - Every autosomal gene has one Paternal and one Maternal copy

Question 29

How are imprinted genes usually found?

Answer 29

Imprinted genes tend to be found in clusters

Question 30

How common are imprinted genes?

Answer 30

Not very common. Very few imprinted genes (~250)

Question 31

What is imprinting mediated by?

Answer 31

By the Imprinting control regions (ICRs)

Question 32

How does imprinted genes work?

Answer 32

- One copy is silenced by DNA methylation catalysed by DNMT3a and Histone methylation leading to inactivation - LmcRNAs are essential to the process - Imprinting patterns are reset during gamete formation

Question 33

What are the two general mechanisms for epigenetic modification?

Answer 33

- DNA methylation - Histone modification

Question 34

What are the two specific mechanisms for epigenetic modification?

Answer 34

- X inactivation - Genetic Imprinting

Question 35

CANCER EPIGENETICS Where is the global DNA methylation altered in tumour cells?

Answer 35

- Hypermethylation of tumour suppressor genes - Hypomethylation of tumour activating genes

Question 36

Where are epigenetic enzymes often mutated?

Answer 36

In tumour cells

Question 37

Give some examples of these Epigenetic enzymes

Answer 37

- Histone Methyltransferases - Histone Acetyltransferases - Histone Kinases - Histone readers - Histone Demethylases

Question 38

Give some examples of Pharmaco - Epigenetic drugs

Answer 38

DNA Methyl Transferase Inhibitors - 5 - Azacytidine (Vidaza) - used to Treat Myelodysplastic syndrome

Question 39

Give some examples of Pharmaco - Epigenetic drugs

Answer 39

Histone Deacetylase Inhibitors - Romidepsin (Istodax) - Used to treat Cutaneous T-cell lymphoma