Epigenetics 1

Question 1

Darwinian theory of evolution?

Answer 1

Organisms with more favorable phenotypes would survive and pass on their traits

Question 2

Lamarck’s theory of evolution?

Answer 2

Animals would evolve during their lifetime (giraffes would get longer necks etc) and pass these traits onto their offspring

Question 3

What is Conrad Waddington’s epigenetic landscape?

Answer 3

Roll marble down valley–> metaphor for cell differentiation
Further down valley = less options to differentiate

Question 4

What is epigenetics (techcl definition)?

Answer 4

The study of changes in phenotype or gene expression caused by mechanisms other than changes in underlying DNA sequence

Question 5

What is epigenetic (essentially definition)?

Answer 5

Layering of info on top of the genome that affects how the genome is used

Question 6

What are some general epigenetic materials?

Answer 6

DNA modifications–> methylation, OHmethylation
Histone modifications
TF complexes

Question 7

Main (non-technical) groups of epigenetic marks?

Answer 7

Writers, readers, erasers

Question 8

What do epigenetic writers do?

Answer 8

Put the epigenetic mark onto the DNA

Question 9

What do epigenetic readers do?

Answer 9

Recognise the mark and respond to it

Question 10

What do epigenetic erasers do?

Answer 10

Remove the marks

Question 11

What characteristic of epigenetics allows cells to be programmed and reprogrammed?

Answer 11

It is v flexible and plastic–> can be changed

Question 12

Open active conformation?

Answer 12

Nucleosomes are in a conformation that allows TFs to access DNA

Question 13

Closed, inatve conformation?

Answer 13

Histones are tightly wound and TFs cant access DNA

Question 14

Permissive state?

Answer 14

DNA and histone modifications are not actively being transcribed–> but available to do so

Question 15

Repressive state?

Answer 15

Chromatin may be in an open conformation but there are histones that may be beginning to close it

Question 16

What does H3K4me3 mean?

Answer 16

The fourth lysine on histone 3 is trimethylated

Question 17

What kind of mark is H3K4me3

Answer 17

active

Question 18

Active marks?

Answer 18

H3K4me3, H3 and H4 acetylation, 5hmC

Question 19

Silent marks?

Answer 19

H3K9me3, H3K27me3, 5mc

Question 20

What can pioneer TFs do?

Answer 20

Recognise their DNA binding site even when chromatin is closed

Question 21

How do pioneer TFs work?

Answer 21

FInd its region on the DNA, open it up and bind to it

Question 22

What is DNA methylation?

Answer 22

Covalent, chemical modification of DNA where a methyl group is added

Question 23

Which enzyme carries out DNA methylation?

Answer 23

DNA methyltransferases (Dnmt)

Question 24

Where is the methyl group taken from in DNA methylation?

Answer 24

S-adenosyl-L-methionine (SAM)

Question 25

Where is the DNA methylated?

Answer 25

Cytosine residues of CpG dinucleotides

Question 26

What are the De novo methyltransferases and what do they do?

Answer 26

Dnmt3a and b Add methylation to areas that didn't previously have it

Question 27

What are the maintenance methyltransferases and what do they do?

Answer 27

Dnmt1 Methylates the unmethylated half os hemi-methylated DNA

Question 28

What is hemi-methylated DNA?

Answer 28

DNA where one strand is methylated and one isnt

Question 29

What are CpG islands?

Answer 29

Areas of v dense CpGs

Question 30

Where are CpG island usually found?

Answer 30

Near promoters