Lecture 2

Question 1

How is Bacterial DNA organized and packed?

Answer 1

Supercoling and nucleoid associated proteins

Question 2

How is Archaeal DNA organized and packed?

Answer 2

small histone fold containing proteins

Question 3

How is eukaryotic DNA organized and packed?

Answer 3

histones forming nocleosomes

Question 4

How many histones form a nucleosome?

Answer 4

8

Question 5

What are histone modifications?

Answer 5

Acetlyation, Phosphorylation, Methylation

Question 6

What is euchormatine and what is heterochromatine?

Answer 6

euchromatine: Active state unwound DNA
heterchromatine: Inactive state condensed DNA

Question 7

What modification can cause euchromatine and which can cause heterchromatine

Answer 7

acteylation: euchormatine
methylation: Heterchormatine

Question 8

What are topoisomerases and what does Topo 1 and Topo 2 do?

Answer 8

Topo 1: removes supercoils by cleaving 1 strand
Topo 2: removes supercolis by cleaving both strands

Question 9

What are TADs?

Answer 9

topological associated domains (chormatine domains)

Question 10

What is cohesine (SMC) and what does it do?

Answer 10

Forms TADs

Question 11

What are chromosome territories?

Answer 11

TADs are localized into Chromosome territories -> euchromatine regions / heterochromatine regions

Question 12

How can you regulate transcription?

Answer 12

Histone exchange

Question 13

3C

Answer 13

3C chromosome conformation capture: Used to look at domains and topological neighbours

Question 14

Hi-C

Answer 14

Higher resolution than 3C

Question 15

Chip-Seq

Answer 15

Protein-DNA interactions are revealed

Question 16

ATAC-Seq

Answer 16

You can look at what chromatine is accessible -> actively transcribed DNA is made visible

Question 17

MNase-Seq

Answer 17

You can look at Nucleosome positions, make libraries with that