The Epigenome

Question 1

What is the genome?

Answer 1

→ The complete set of genetic material in a cell

→ DNA sequence present in a full set of chromosomes

Question 2

What forms the first level of packing?

Answer 2

→ Histone proteins forming nucleosomes

Question 3

What are the features of euchromatin?

Answer 3

→ Gene rich
→ transcriptionally active
→ nucleosomes are far apart

Question 4

What are the features of heterochromatin?

Answer 4

→ Gene poor
→ less transcriptionally active
→ condensed appearance
→ repetitive DNA

Question 5

Describe the packaging of DNA

Answer 5

→ Nucleosomes wound to make 30nm fibres
→ fibres wound up further with scaffold proteins
→ chromosomes are most densely packed

Question 6

What is the epigenome?

Answer 6

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

Question 7

What does an epigenetic change result in?

Answer 7

→ A change in the phenotype but not genotype

Question 8

What are the 4 epigenetic mechanisms?

Answer 8

→ DNA methylation
→ histone modification
→ X inactivation
→ Genomic imprinting

Question 9

What is DNA methylation and what does it require?

Answer 9

→ The addition of a methyl group in the 5’ position of cytosine
→ DNA methyltransferase
→ S-adenosyl methionine to provide the methyl group

Question 10

How is DNA methylation done?

Answer 10

→ DNA methyltransferase enzymes

Question 11

What are the DNA methyltransferase enzymes?

Answer 11

→ DNMT1
→ DNMT3a
→ DNMT3b

Question 12

In differentiated cells where does DNA methylation occur?

Answer 12

→ in CpG nucleotides (C next to a G)

Question 13

When does passive demethylation occur?

Answer 13

→ During replication

Question 14

What is passive demethylation done by?

Answer 14

→ TET enzymes - ten eleven translocation enzymes

→ TDG - thymidine DNA glycosylase

Question 15

What is the function of TET enzymes?

Answer 15

→ They catalyse the movement from 5 methylcytosine to hydroxy methyl cytosine to formyl to carboxy

Question 16

What is the effect of DNA methylation?

Answer 16

→ Turns transcription off by preventing the binding of transcription factors

Question 17

What is a CpG island?

Answer 17

→ A region of DNA where CpG is more frequent than normal

Question 18

What is histone modification?

Answer 18

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

Question 19

What are common histone modifications?

Answer 19

→ Acetylation and methylation

Question 20

What are modifications named based on?

Answer 20

→ Histone
→ amino acid
→ actual modification

Question 21

What does a H3K4Me3 mean?

Answer 21

→ on histone 3

→lysine at position 4 is trimethylated

Question 22

What are the three types of histone modification enzymes?

Answer 22

→ Writers
→ Erasers
→ Readers

Question 23

What are examples of 2 writer enzymes?

Answer 23

→ Histone acetyltransferase - HAT1

→ Histone methyltransferase - EHMT1

Question 24

What are 2 examples of eraser enzymes?

Answer 24

→ Histone deacetylase - HDAC1

→ Histone demethylase - KDM1

Question 25

What are 2 examples of reader enzymes?

Answer 25

→ Bromodomain and extra terminal (BET) proteins - BRD2 | → Chromodomain proteins - CBX1

Question 26

What is the effect of histone acetylation at lysine residues?

Answer 26

→ Relaxes the chromatin structure and makes it accesible to transcription factors

Question 27

Why does chromatin relax when acetyl is added at lysine residues?

Answer 27

→ Lysine is basic | → if you add an acetyl (acid) group it relaxes the chromatin

Question 28

What is the effect of histone methylation?

Answer 28

→ Can repress or activate transcription depending on where it occurs

Question 29

How can histone modifications occur and what happens as a result?

Answer 29

→ at the same time (concurrently) | → their effects can interact or modify each other

Question 30

Why does X inactivation occur?

Answer 30

→ ensures that every somatic cell in humans has the same number of active copies of every gene

Question 31

Why is X inactivation needed?

Answer 31

→ Y chromosome has virtually no genes | → only one copy of X in males

Question 32

Describe how X inactivation occurs?

Answer 32

→ Xist gene is transcribed as long noncoding RNA from the X inactivation centre → It then binds all over the X chromosome → histone acetylation is removed and histone methylation occurs

Question 33

What are inactive X chromosomes called?

Answer 33

→ inactive X chromosomes are heterochromatic - Barr body

Question 34

What is Tsix and what does it do?

Answer 34

→ It is derived by transcription in the opposite direction and antagonises Xist RNA to keep one X active

Question 35

Give an example of X inactivation in cats?

Answer 35

→ all tortoiseshell cats are female → they 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 36

What is imprinting?

Answer 36

→ The selective expression of genes related to the parental origin of the gene copy

Question 37

Where do imprinted genes tend to be found?

Answer 37

→ in clusters

Question 38

What are imprinted genes mediated by?

Answer 38

→ Imprinting control regions

Question 39

What mechanism causes imprinting?

Answer 39

→ One copy is silenced by DNA methylation | → catalysed by DMNT3a and histone methylation leading to inactivation

Question 40

When are imprinting patterns reset?

Answer 40

→ During gamete formation

Question 41

How are epigenetics altered in cancer cells?

Answer 41

→ hypermethylation of tumor suppressor genes | → hypomethylation of tumor activating genes

Question 42

What enzymes are mutated in tumor cells?

Answer 42

``` → DNMT3a and TET1/2 → Histone acetyltransferases → Histone methyltransferases → Histone kinases → histone readers → histone demethylases ```

Question 43

What are 2 DNA methyltransferase inhibitors?

Answer 43

→ 5 azacytidine | → Myelodysplastic syndrome

Question 44

What are 2 histone deacetylase inhibitors?

Answer 44

→ Romidepsin | → Cutaneous T-cell lymphoma