Epigenetics

Question 1

What is chromatin?

Answer 1

Complex of DNA and proteins into which eukaryotic chromosomes are packaged

Question 2

What is included in a nucleosome?

Answer 2

An octomeric histone core with 2 subunits of H2A, H2B, H3, and H4, with 147 base pairs of DNA

Question 3

What are histones?

Answer 3

Positively charged DNA binding proteins with flexible tails

Question 4

What is linker DNA?

Answer 4

DNA between histones

Question 5

What do H1 histones do?

Answer 5

Linker histones that are involved in the assembly of nucleosomes into higher order structures

Question 6

What are the two types of chromatin?

Answer 6

Euchromatin and heterochromatin

Question 7

What is heterochromatin? Is it being transcribed?

Answer 7

Chromatin that is highly dense and compacted. It is not being transcribed

Question 8

What is euchromatin? Is it being transcribed?

Answer 8

Chromatin that is more loosely packaged. Is being transcribed

Question 9

Is chromatin always either euchromatin or heterochromatin?

Answer 9

No, it’s a lot more complicated and chromatin can quickly shift between the two

Question 10

What are 3 common histone modifications?

Answer 10

Methylation, acetylation, and phosphorylation

Question 11

What is histone acetylation?

Answer 11

Acetyl groups are added to lysine residues in the histone tails. They are rapidly reversible

Question 12

What type of enzyme adds acetyl groups to histones?

Answer 12

Histone acetylases (HATs)

Question 13

What type of enzyme removes acetyl groups from histones?

Answer 13

Histone deacetylases (HDACs)

Question 14

Does histone acetylation typically activate or repress gene expression?

Answer 14

Activate

Question 15

Does histone methylation typically activate or repress gene expression?

Answer 15

Can be either

Question 16

What are 3 factors that determine whether histone methylation activates or represses gene expression?

Answer 16

1. Which amino acids in the histone tail gets methylated
2. Which gene
3. Any other modifications

Question 17

Is H3K9 methylation associated with activated or repressed gene expression?

Answer 17

Repressed

Question 18

Is H4K4 methylation associated with activated or repressed gene expression?

Answer 18

Activated

Question 19

What are writer enzymes?

Answer 19

Enzymes that add histone modifications

Question 20

What are eraser enzymes?

Answer 20

Enzymes that remove histone modifications

Question 21

What are reader enzymes?

Answer 21

Enzymes that recognize histone modifications

Question 22

What are 3 mechanisms by which histone modifications change gene expression?

Answer 22

1. Recruit nucleosome and chromatin remodelling proteins to change promoter accessibility
2. Changing DNA accessibility
3. Recruiting TFs

Question 23

Are nucleosomes randomly distributed through the genome?

Answer 23

Nope

Question 24

What is nucleosome positioning?

Answer 24

A measure of how often a nucleosome is in a particular spot at a particular time

Question 25

What are 3 ways to describe nucleosome positioning?

Answer 25

Perfect, partial, or no positioning

Question 26

What is perfect nucleosome positioning?

Answer 26

The nucleosome is always in the same spot in every cell of a certain type under certain conditions

Question 27

What is partial nucleosome positioning?

Answer 27

The nucleosome is often, but not always in the same spot in every cell of a certain type under certain conditions

Question 28

What is no nucleosome positioning?

Answer 28

Random

Question 29

What regions of the genome tend to be nucleosome poor?

Answer 29

Where things bind. Promoters, enhancers, terminators

Question 30

Where would perfect positioning be found?

Answer 30

Next to nucleosome poor regions

Question 31

What is nucleosome occupancy?

Answer 31

How frequently a locus tends to be occupied by nucleosomes, and how many

Question 32

How much genomic DNA is occupied by nucleosomes?

Answer 32

Most of it

Question 33

What sorts of regions have low nucleosome occupancy?

Answer 33

Functional regions

Question 34

What is a poised/closed enhancer?

Answer 34

The histones have a modification that allows for the enhancer to be accessible, but also another one that prevents that. The enhancer becomes available for binding once the repressing modification is removed

Question 35

What is a latent enhancer?

Answer 35

When the histones need a certain modification to become accessible, and do so once they receive that modification

Question 36

What do antirepressor transcription factors do?

Answer 36

Have the ability to overcome the repressive effects of chromatin and activate transcription, even when the chromatin is in a repressive state

Question 37

What are 5 factors that influence nucleosome positioning?

Answer 37

1. DNA sequence. A and T rich sequences aren't bound by nucleosomes as much 2. Histone modifications 3. Nucleosome remodelling enzymes 4. RNAP II and GTFs 5. TFs

Question 38

Why is competent chromatin structure necessary, but not sufficient for transcription to occur?

Answer 38

Still need RNAP II and the GTFs. But chromatin has to be competent for them to bind in the place