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CMB2001-Eukaryotic Gene Expression > CMB2001/L03 Chromatin Structure > Flashcards

CMB2001/L03 Chromatin Structure Flashcards

1
Q

What is chromatin composed of?

A

Basic histone proteins

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2
Q

What is the primary function of chromatin?

A

To compact DNA

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3
Q

Give the 2 types of histones.

A

Core histones
Linker histones

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4
Q

Describe the N-terminal tail domain of histones. (2)

A

Highly basic
Rich in Lys and Arg

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5
Q

Describe the globular domain of histones.

A

a-helices and loops

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6
Q

What are the repeating units of core histones?

A

Nucleosomes

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7
Q

Define a nucleosome.

A

-147bp of DNA wrapped twice around an octamer of histone proteins

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8
Q

Define an octamer.

A

Central H3-H4 tetramer + 2 flanking H2A-H2B dimers

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9
Q

How are nucleosomes organised? (3)

A

DNA passes directly from one nucleosome to the next
Linker histones (e.g., H1) bind to DNA between nucleosomes
In vitro linker histones result in formation of thicker 30nm fibre

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10
Q

What structure of chromatin is unlikely to exist in vivo?

A

Folded 30nm fibre

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11
Q

What evidence suggests that chromatin inhibits transcription?

A

RNA pol II + TFs + naked DNA template -> transcription
RNA pol II + TFs + chromatin template -> no transcription
Nucleosomes are disrupted or lost during transcriptional activation

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12
Q

How do genetic studies in Saccharomyces cerevisiae show that chromatin inhibits transcription? (5)

A

H4 gene copies were deleted
Plasmid expressing H4 under control of regulatable GAL4 promoter
ON with galactose but OFF with glucose
When glucose was added, H4 expressed shut off
Nucleosome depletion and expression of inducible genes

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13
Q

Give the 2 conflicting roles of the nucleosome.

A

Compaction of DNA
Forms a template for DNA transcription

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14
Q

Give the 3 major mechanisms for modulating chromatin structure.

A

Histone variants
Post-translational modification of histones
ATP-dependent chromatin remodelling

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15
Q

What level are histone variants expressed at?

A

Very low levels compared to conventional counterparts

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16
Q

Which is the only histone without a variant?

A

H4*
Recently described in humans as variant H4G

17
Q

Give a variant of histone H2A.

A

H2AZ
H2AX
macroH2A

18
Q

Give a variant of histone H2B.

19
Q

Give a variant of histone H3.

A

CENP-A
H3.3

20
Q

Where does most post-translational modification of histones occur?

A

In the N-terminal tail

21
Q

Give the 4 methods of post-translational modification in histones.

A

Acetylation
Methylation
Ubiquitylation
Phosphorylation

22
Q

How could histone modification constitute a code that sets its transcriptional state?

A

Directly alter chromatin folding/structure
Control recruitment of non-histone proteins to chromatin (influence recruitment/function of transcriptional machinery)

23
Q

What is histone lysine acetylation and deacetylation mediated by?

A

Histone acetyl transferases (HATs)
Histone deacetylases (HDACs)

24
Q

Why is the acetylation state of histones highly dynamic?

A

Acetylation is readily reversibly by HDACs

25
Q

How is yeast Gcn5 known to function? (2)

A

Homologous to first nuclear HAT
Transcriptional activator

26
Q

Give the 2 types of nuclear HAT large multisubunit complexes.

A

GNAT family
MYST family

27
Q

Give the catalytic subunit and substrate of yeast SAGA (GNAT).

A

CS: yGCN5
S: H3/H2B

28
Q

Give the catalytic subunit and substrate of human STAGA (GNAT).

A

CS: hGCN5
S: H3/H2B

29
Q

Give the catalytic subunit and substrate of human PCAF (GNAT).

A

CS: PCAF
S: H3/H4

30
Q

Give the catalytic subunit and substrate of yeast NuA4 (MYST).

A

CS: Esa1
S: H4/H2A

31
Q

Give the catalytic subunit and substrate of human Tip60 (MYST).

A

CS: Tip60
S: H4/H2A

32
Q

How are HATs recruited?

A

By activators to specific promoters
Some part of general transcription machinery

33
Q

How does acetylation mediate transcriptional activation? (2)

A

Direct influence on chromatin structure
Directs recruitment of bromodomain proteins

34
Q

How does acetylation affect the charge of lysine and what effect does this have on chromatin structure?

A

Reduced charge of lysine (+ to 0)
Allows chromatin fibre to compact

35
Q

How do bromodomains affect chromatin structure? (2)

A

Specific acetylated lysine residues recognised by proteins with bromodomains
Often promote transcription

36
Q

Which 2 amino acids can histone methylation occur on?

A

Lysine and Arginine

37
Q

What enzymes methylate lysines?

A

Histone Lysine Methyl Transferases (HKMTs)

38
Q

How can methylated lysines affect transcription?

A

Function as activating or repressing marks

CMB2001-Eukaryotic Gene Expression (10 decks)

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