L5 - DNA Modifications

Question 1

What is the purpose of an epigenetic clock?

Answer 1

Used to determine a person’s chronological age based on changes in DNA methylation patterns at specific genomic locations (CpGs).

Question 2

How many CpG sites are there in the human genome?

Answer 2

28 million (potential for cytosine methylation)

Question 3

What is the donor of the methyl group called?

Answer 3

S-adenosyl-L-methionine (SAM)

Question 4

What is the role of the DNA methyltransferase DNMT1?

Answer 4

It maintains DNA methylation patterns during cell division. On the newly synthesised strand after DNA replication, it will add the methyl groups where there were previously on the old strand.

Question 5

What is the role of DNMT3A and DNMT3B?

Answer 5

These are de novo methyltransferases which establish new methylation patterns during early development and cellular differentiation. Addition of methyl groups to previously unmethylated CpG sites.

Question 6

What is a possible reason for methylation of DNA?

Answer 6

DNA is often from ancient retroviruses which were active over evolutionary time and methylation keeps repetitive DNA elements shut down

Question 7

Where are CpG islands mainly found?

Answer 7

At promoters of most human genes

Question 8

What will happen to the gene if the CpG island is methylated?

Answer 8

It will lead to silencing of that gene. Methylation of promoters tends to lead to gene inactivity.

Question 9

What is an importance of 5hmC (5-hydroxymethyl-cytosine)?

Answer 9

Erasure of DNA methylation marks that are inherited from the parental germline. An important regulator of gene expression and cellular function. It is an intermediate during the process of demethylation.

Question 10

What is passive DNA methylation?

Answer 10

Loss of 5mC during successive rounds of replication in the absence of functional DNA methylation maintenance machinery.

Question 11

What is the purpose of bisulfite sequencing?

Answer 11

Detection of cytosine methylation in DNA

Question 12

How does it work?

Answer 12

Bisulfite treatment converts unmethylated cytosines into uracils. PCR amplification and sequencing distinguishes between unmethylated (T) and methylated (C) cytosines at single nucleotide resolutions. Polymerases read the strand and see the uracil as a thymine.

Question 13

What is a limitation with this?

Answer 13

Bisulfite sequencing does not distinguish between 5mC (5-methyl cytosine) and 5hmC (5-hydroxy methyl cytosine)

Question 14

e.g - The ability of a daughter cell to retain a memory of the gene expression patterns that were present in the parent cell. What is this an example of?

Answer 14

Epigenetic inheritance

Question 15

Which genetic disorder is caused by methylation at the FMR1 gene?

Answer 15

Fragile-X Syndrome

Question 16

Where does methylation occur here?

Answer 16

Extended repeats of CGG are found at the UTR and this expansion can cause an epigenetic response and cause the gene to be switched off

Question 17

What drug can be used to reactivate FMR1?

Answer 17

Chemotherapy drug which inhibits the action of DNMT1

Question 18

How can azacytidine & decitabine be useful as drug-induced passive DNA methylation substances?

Answer 18

They are cytosine nucleoside analogues which form covalent bonds with DNMTs during DNA replication causing their inhibition. Successful in treating certain types of leukaemia.

Question 19

What is meant by the static/conserved model?

Answer 19

Epigenetic marks established early in the development are stably maintained throughout the lifespan of the cell or organism. Epigenetic marks act as a “memory” of past events or exposures, such as environmental stressors or developmental cues.

Question 20

What is meant by the dynamic equilibrium model?

Answer 20

Continuous de novo methylation and demethylation (mainly in ES cells)