Epigenetics and cancer

Question 1

Define epigenetics.

Answer 1

Meiotically and mitotically heritable changes in the gene expresion that are not coded by the sequence itself.

Question 2

How much DNA is wrapped around an octomer?

Answer 2

146 bp are wrapped around twice.

Question 3

What are nucleosome remodelling enzymes?

Answer 3

Large (2 kDa) protein complexes, which in an ATP dependant manor reposition nucleosomes to expose different sections of DNA. This are not sequence specific so need to be recuited by other proteins like transcription factors. The families are SWI/SNF and ISWI.

Question 4

How do histone tails become acetylated and what is the effect of this?

Answer 4

Lysine residues are neutrised by the addtion of a acetyl group and so does not interact with negative DNA as well and the chromatin structure opens. Additionally acetylated lysine group provide interacting sites for specific proteins. HATS add the acetyl group using acetyl-coenzyme A as a donor. HDAC remove the acetyl groups.

Question 5

Which drugs inhibit HDACs?

Answer 5

trichostatin A, butyrate.

Question 6

Who do HATS and HDAC get to DNA?

Answer 6

They are often recruited by transcription factors. HATS are not sequence specific.

Question 7

Give three examples of HATS.

Answer 7

Gcn5, PCAF and p300/CBP.

Question 8

What do acetylated lysine groups recruit?

Answer 8

Proteins which bromodomains including more HATs like p300/CBP. this pull in more proteins. Also nucleosome remodelling enzymes.

Question 9

How does acetylated lysine marks directly lead to active transcription of genes.?

Answer 9

They recruit bromodomain proteins including p300/CBP which then recruited the mediator complex and basal transcription factors which act as a bridge to the recruited RNA Pol II which is then phosphorylated at the C-terminal domain and becomes active.

Question 10

How are lysine residues of histone tails methylated?

Answer 10

histone methyl transferases (HMTs) add methyl groups from the donor S-adenosyl methionine to lysines to even mono- di- or tri-methylate. Demethylases remove the methyl groups.

Question 11

Which lysines of H3 tails are active when methylated?

Answer 11

K4 (K39 and K79)

Question 12

Which lysines of H3 tail are repressive when methylated?

Answer 12

K9 and K27.

Question 13

Which HMT methylates K4?

Answer 13

MLL

Question 14

Which HMT methylates K9?

Answer 14

Suv39

Question 15

Which HMT methylates K27?

Answer 15

PRC2.

Question 16

What is K27 methylation premeraly involved in

Answer 16

The silencing of genes in stem cell differentiation.

Question 17

What is K9 methylation primarily involved in?

Answer 17

The constitutive condensing of DNA at e.g. centromers or telomeres.

Question 18

What binds H3K9me?

Answer 18

HP1 (important in condensing chromation)

Question 19

What binds H3K27me?

Answer 19

PCR1.

Question 20

What is PRC2?

Answer 20

A HMT, contains EZH2 one which has a SET domain that carries out the methylation. It also contains the associated proteins SUZ12 and EED.

Question 21

What does PRC1 do?

Answer 21

Binds H3K27me with polycomb ring fingers and ubiquitinates H2AK119 residue.

Question 22

Which enzyme copied the DNA methylation pattern onto the new palamdromic strand after DNA replication.

Answer 22

DNMT1 and others a bit like it.

Question 23

Describe the feedback mechanism loop which allows repressive chromatin to spread.

Answer 23

Me-CpG is bound by MBD proteins. These recuites HDAC and HMTS inculing Suv39 which methylates H3K9. H3K9me is then able to recruit HP1 leading to transcriptional silencing. Suv39 also recruits DNMTs to futher methylate CpGs and finish the loop.

Question 24

How many promoter regions are CpG islands and are the generally methylated or unmethylated?

Answer 24

60% and unmethylated, mostly remain unmethylated even when not expressed.

Question 25

Give to examples of tumour suppressor genes which may have methylated promoters in cancer.

Answer 25

RB in retinoblastoma, APC in colorectal and other cancers.

Question 26

How will we turn silenced tumour suppressor genes back on?

Answer 26

By stopping DNA methylation and inducing histone acetylation.

Question 27

Describe experiments which tried to resensitive ovarian cancer cell tumours in mice to cisplatin.

Answer 27

Carried the silenced tumour supressor gene MLH1 (involved in DNA repair and apoptosis induced by p53) due to methylated CpG island promoter. Firstly used the DNMT inhibitor decitabine to resensitise; worked in vivo xenograft model but failed phase I safety clinical train. Then decied to use this and a HDAC inhibitor before cisplatain which was better and now in clinical trail. Increases expression of MLH1 to restore sensitivity.

Question 28

What are some other targets of drugs being developed?

Answer 28

HDACs, DNMTs, bromodomain interactions, HMTs.