CMB2001/L04 Chromatin & Transcription

Question 1

Give the 4 main mechanisms that control chromatin structure.

Answer 1

Acetylation
Methylation
Ubiquitylation
Phosphorylation

Question 2

Which remodelling complex is held by all cells?

Answer 2

Snf2-related ATPase

Question 3

What is SF2?

Answer 3

Helicase and NTP-driven nucleic acid translocase superfamily 2

Question 4

Give the 5 stages of ATP-dependent chromatin remodelling.

Answer 4

Sliding
Unwrapping
Eviction
Spacing
Histone variant exchange

Question 5

What is Snf2?

Answer 5

Catalytic subunit of SWI/SNF

Question 6

What does Snf2 do?

Answer 6

Hydrolyses 1000 ATP molecules per minute in presence of DNA or nucleosomes

Question 7

Describe how SWI/SNF acts as a molecular motor.

Answer 7

Uses energy from ATP hydrolysis to track along DNA and induce torsion

Question 8

What is the homologue of SWI/SNF in yeast?

Answer 8

GCN5 HAT

Question 9

What is the function of bromodomains in Snf2?

Answer 9

Tethering to acetylated nucleosomes

Question 10

Where are HATs and ATP-dependent remodellers commonly recruited?

Answer 10

To the same promoters

Question 11

Name 3 SWI/SNF complexes in humans.

Answer 11

PBAF
cBAF
ncBAF

Question 12

Give 2 roles of SWI/SNF complexes in humans.

Answer 12

General transcription
Cell cycle control via interaction with Rb & cyclin E
Development, deletion in mice results in embryonic lethality
Tumour suppression pathways

Question 13

Explain how SWI/SNF is related to cancer.

Answer 13

Different mutations confer distinct vulnerabilities in mouse models
Tumour suppressor activity most likely due roles in facilitating transcription factor function

Question 14

How do cells repress transcription?

Answer 14

Exploiting chromatin structure

Question 15

What is chromatin structure mediated by to repress transcription?

Answer 15

Histone deacetylases (HDACs)
ATP-dependent remodellers
Histone methylases (heterochromatin)

Question 16

What are the 4 major groups of histone deacetylases?

Answer 16

Class I-IV
Class III Sir2 family (SIRTUINS) require NAD as a cofactor

Question 17

What are active and repressed regions of the genome described as?

Answer 17

Hyper/hypoacetylated

Question 18

What is deacetylated of the genome mediated by?

Answer 18

Histone deacetylases
Act as corepressors

Question 19

How do HDACs usually function?

Answer 19

In the context of large multi-subunit complexes

Question 20

How are HDAC co-repressor complexes recruited to promoters?

Answer 20

By interaction with site-specific DNA binding proteins

Question 21

What is the function of the NuRD complex?

Answer 21

Roles in normal differentiation and tumourogenesis

Question 22

Which family does the NuRD complex belong to?

Answer 22

Mi2/CHD family

Question 23

What is euchromatin? (2)

Answer 23

Gene-rich
Potential to be transcribed

Question 24

What is heterochromatin? (3)

Answer 24

Gene-poor
Repetitive regions
Transcriptional silencing
E.g., centromeres and telomeres

Question 25

Give 3 biochemical features of heterochromatin.

Answer 25

Hypoacetylation Specific histone H3 methylation Association of specific silencing factors

Question 26

Describe the assembly of heterochromatin. (4)

Answer 26

Histone modifications Binding of HP1 Nucleosome compaction Recruitment of additional factors

Question 27

What kind of protein is heterochromatin protein 1?

Answer 27

A chromodomain protein

Question 28

What do chromodomains often recognise and bind?

Answer 28

Methylated lysine residues

Question 29

What is the chromodomain of HP1 specific for?

Answer 29

H3 Lys9me2/3

Question 30

What does the binding of HP1 trigger? (2)

Answer 30

Compacting of nucleosomal arrays Recruitment of further activities that prevent recruitment/activity of RNA pol II

Question 31

Describe the analysis of heterochromatin using reporter silencing analysis using ade6.

Answer 31

Normal wild-type - ade6 gene expressed white colonies Silencing reported strain - ade6 silenced red colonies (red pigment from build up of adenine biosynthetic intermediate) Mutation in gene encoding a component of heterochromatin - ade6 silencing alleviated white/pink colonies

Question 32

How is the number of X-linked genes equalised in males and females?

Answer 32

X chromosome inactivation

Question 33

By which proteins are Barr body formation controlled? (3)

Answer 33

Non-coding RNAs, Xist and Tsix

Question 34

Describe the process of X chromosome inactivation. (5)

Answer 34

Later development - Xist upregulated Xist coats chromosome Xist recruits H3K27 methylase Recruitment of further silencing factors Inactive X (Xi)