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 is Tsix and what does it do?

Answer 33

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

Question 34

What are inactive X chromosomes called?

Answer 34

Inactive X chromosomes are heterochromatic - Barr body

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 ability of a gene to be expressed depends upon the sex of the parent who passed on the gene → Functionally hemizygous - Willis syndrome

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 → Catalyzed by DMNT3a and histone methylation leading to inactivation → Requires SAM which is involved in methylation reactions

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

Question 45

What is the role of histone readers?

Answer 45

Protein complexes that read combinations of marks: chromodomains specifically recognize methylated residues, while bromodomains bind acetylated residues