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CMB2001-Eukaryotic Gene Expression > CMB2001/L04 Chromatin & Transcription > Flashcards

CMB2001/L04 Chromatin & Transcription Flashcards

1
Q

Give the 4 main mechanisms that control chromatin structure.

A

Acetylation
Methylation
Ubiquitylation
Phosphorylation

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2
Q

Which remodelling complex is held by all cells?

A

Snf2-related ATPase

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3
Q

What is SF2?

A

Helicase and NTP-driven nucleic acid translocase superfamily 2

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4
Q

Give the 5 stages of ATP-dependent chromatin remodelling.

A

Sliding
Unwrapping
Eviction
Spacing
Histone variant exchange

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5
Q

What is Snf2?

A

Catalytic subunit of SWI/SNF

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6
Q

What does Snf2 do?

A

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

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7
Q

Describe how SWI/SNF acts as a molecular motor.

A

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

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8
Q

What is the homologue of SWI/SNF in yeast?

A

GCN5 HAT

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9
Q

What is the function of bromodomains in Snf2?

A

Tethering to acetylated nucleosomes

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10
Q

Where are HATs and ATP-dependent remodellers commonly recruited?

A

To the same promoters

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11
Q

Name 3 SWI/SNF complexes in humans.

A

PBAF
cBAF
ncBAF

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12
Q

Give 2 roles of SWI/SNF complexes in humans.

A

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

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13
Q

Explain how SWI/SNF is related to cancer.

A

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

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14
Q

How do cells repress transcription?

A

Exploiting chromatin structure

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15
Q

What is chromatin structure mediated by to repress transcription?

A

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

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16
Q

What are the 4 major groups of histone deacetylases?

A

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

17
Q

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

A

Hyper/hypoacetylated

18
Q

What is deacetylated of the genome mediated by?

A

Histone deacetylases
Act as corepressors

19
Q

How do HDACs usually function?

A

In the context of large multi-subunit complexes

20
Q

How are HDAC co-repressor complexes recruited to promoters?

A

By interaction with site-specific DNA binding proteins

21
Q

What is the function of the NuRD complex?

A

Roles in normal differentiation and tumourogenesis

22
Q

Which family does the NuRD complex belong to?

A

Mi2/CHD family

23
Q

What is euchromatin? (2)

A

Gene-rich
Potential to be transcribed

24
Q

What is heterochromatin? (3)

A

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

25
Q

Give 3 biochemical features of heterochromatin.

A

Hypoacetylation
Specific histone H3 methylation
Association of specific silencing factors

26
Q

Describe the assembly of heterochromatin. (5)

A

Histone modifications
Binding of HP1
Nucleosome compaction
Nucleosome compaction
Recruitment of additional factors

27
Q

What kind of protein is heterochromatin protein 1?

A

A chromodomain protein

28
Q

What do chromodomains often recognise and bind?

A

Methylated lysine residues

29
Q

What is the chromodomain of HP1 specific for?

A

H3 Lys9me2/3

30
Q

What does the binding of HP1 trigger? (2)

A

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

31
Q

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

A

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

32
Q

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

A

X chromosome inactivation

33
Q

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

A

Non-coding RNAs, Xist and Tsix

34
Q

Describe the process of X chromosome inactivation. (5)

A

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

CMB2001-Eukaryotic Gene Expression (11 decks)

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