10th Feb - How structures have helped us understand gene regulation in a chromatin environment

Question 1

What do PHD domains bind to?

Answer 1

Methyl lysines in a surface groove

Question 2

What do Chromodomains bind to?

Answer 2

Methyl lysines in a deep groove

Question 3

What do bromodomains bind to?

Answer 3

They recognise acetyl lysines in a deep pocket with matching chemistry

Question 4

What is the function of combinatorial recognition?

Answer 4

Creates greater specificity

Question 5

Outline MSL-3 binding to the DNA

Answer 5

The chromodomain recognises a combination of the DNA minor groove and mono-methyl K16 in histone H4
Variant bromodomains can simultaneously recognise two acetyl lysines

Therefore will only recognise H4K5acK8ac

Question 6

Outline ATRX binding to DNA

Answer 6

The ADD domain (PhD and GATA and Zn fingers) recognises a combination of unmethylated K4 and di or tri methylated K9 in H3

Question 7

Which domains recognise nucleosomes?

Answer 7

WD40 domain from RCC1

BAH domain from Sir3

Question 8

Why are SMRT KO mice lethal?

Answer 8

Due to cardiogenesis defects

Question 9

How does LSD1 bind to the H3 tail?

Answer 9

Through Co-REST’s binding

Question 10

What catalyses the ‘2nd step’ in repressing chromatin?

Answer 10

PRC2

Question 11

What is the function of ISW1A?

Answer 11

Move nucleosomes, thus regulate nucleosome spacing