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Health and Disease: Genes > Boyes Epigenetics > Flashcards

Boyes Epigenetics Flashcards

1
Q

What do epigenetic factors do?

A

Bring about an inheritable change in expression of a gene without introducing mutation

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2
Q

What is the structure of a nucleosome?

A

H3/4 tetramer, 2xH2A/B dimers, H1 at entry and exit points.
147bp wrapped around with dyad 80p in
50 nucleotide linker

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3
Q

How many times does DNA wrap around the histone?

A

1.65 turns

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4
Q

What is the structure of a histone protein?

A

High R/K proportion, 2alpha helices conected by loops

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5
Q

How does the nucleosome remodelling complex work?

A

DBD binds entry point to push, forming loop
translocation domain binds at the dyad to pull 10bp via hinge
uses ATP

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6
Q

What increase in DNase1 hypersensitivity is found at promoters?

A

100x

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7
Q

How can promoters be mapped?

A

DNase digestion at promoters then restriction digests at known points, to find promoters based on size of fragment. Known as indirect end labelling

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8
Q

What is indirect end labelling?

A

Method of finding promoter sites

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9
Q

What additional functions do nucleosome remodelling complexes have?

A

spacing following replication
exposure of DNA
exchange of H2A/B dimerss

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10
Q

How are nucleosome remodelling complexes classified?

A

By ATPase subunit

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11
Q

What are the classes of remodelling complex?

A

SNI/SWF, ISWI, CHD, INO80

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12
Q

What is the structure of nucleosome remodelling complexes?

A

2-15 subunits, up to 2MDa
ATPase and helicase domains
other targetting domains

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13
Q

How can nucleosome remodelling complexes be recruited to a promoter?

A

Via activators or direct to chromatin

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14
Q

Where is the ovalbumin gene activated?

A

Oviduct

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15
Q

Where is the vitellogenin gene stimulated?

A

By oestrogen in the liver

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16
Q

How are X chromosomes inactivated?

A

DNA methylation of CpG islands in promoters

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17
Q

Does epigenetic memory exist in Drosphilia flies?

A

Yes, even though they do not have DNA methylation

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18
Q

What timescale can epigenetics occur on?

A

Accumulate over a lifetime

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19
Q

What methylation state does newly replicated DNA exist in?

A

Hemi-methylated

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20
Q

Which Dnmt is responsible for methylation after replication?

A

Dnmt1

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21
Q

Which enzyme is responsible for DNA methylation de novo?

A

Dnmt3a/b

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22
Q

When does Dnmt3 act?

A

During embryonic development

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23
Q

What is the structure of Dnmt?

A

Highly conserved catalytic C terminal domain

N terminal binds to other proteins

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24
Q

When is Dnmt1 recruited?

A

PCNA clamp association at replication fork

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25
Q

When is Dnmt3 not recruited?

A

When 3L regulatory unit dissociates

26
Q

How are CpG islands protected from methylation?

A

Transcription by Pol 2 Ser5 recruits Set1 and Cfp1 to promoter
H3K4me3 opens chromatin structure
no association of 3L to dnmt3

27
Q

Which novel proteins can be isolated from a promoter?

A

Set1 and cfp1

28
Q

How can Set1 and Cfp1 be isolated from promoters?

A

HinP1 methylation sensitive digestion of GCGC sites

29
Q

What is the structure of CpG islands?

A

1kb streches of G rich

30
Q

Where are CpG islands found?

A

All housekeeping genes and 40% of tissue specific genes

31
Q

How many CpG islands are the hapliod human genome?

A

25,500

32
Q

What frequency are CpG islands?

A

1/10

33
Q

What type of CpG islands have differential expression?

A

Weak promoters 1/20

34
Q

What CpG frequency has no effect on transcription?

A

1/100

35
Q

How does methylation repress transcription?

A

Directly by blocking major groove binding sites or indirectly by binding MBPs.
MECP1/2 has HDAC/Sin3a activity

36
Q

When does CpG island methylation occur?

A

X chromosome inactivation and cancerous mutations

37
Q

How can CpG islands be detected?

A

Bisulphite sequencing deaminates C to U, so only C left for sequencing are mC
Digestion with Msp1 (non specific) and Hpa11 (unmeth)

38
Q

What is the histone code hypothesis?

A

Predicts that distinct combinations of modifications act to control chromatin structure and gene expression

39
Q

Where do histone modifications act?

A

Exposed Lysine tails

40
Q

Where does acetylation occur?

A

H3K14 binds bromodomains

H3K16 prevents compaction to a 30nm fibre

41
Q

What type of proteins have bromodomains?

A

Coactivator/HATs associated with Pol2 elongator form

Remodelling complexes SWI/SNF and RSC which displaces H2A/B dimers

42
Q

How is acetylation removed?

A

HDACs recruited after the Pol2 has passed

43
Q

How can acetylation be observed?

A

Removal of nucleosomes alters sedimentation in centrifugation
Increased DNas1 sensitivity

44
Q

How does acetylation activate chromatin?

A

Neutralises DNAphos - K/R interactions

45
Q

Is acetylation epigenetic?

A

NO

46
Q

How is H3K4me3 produced?

A

Set1 methyltransferase associated with Pol2 CTD phospho-ser5 at promoters

47
Q

What type of domain does H3K4me3 recruit?

A

plant homeodomain (PHD) in remodelling complexes and HATs

48
Q

Which histone methylations are activating?

A

K4, K36

49
Q

Where is H3K4me1 found?

A

Active enhancers

50
Q

Where is H3K36me3?

A

In gene body, associated with Set2 (Ser2)

51
Q

How does H3K36 act?

A

Recruits HDACs to reset chromatin after transcription

52
Q

What type of methylation does HP1 oproteins bind?

A

Chromodomains bind H3K9

53
Q

How is H3K9 maintained?

A

Chromodomains of HP1 bind and recruit Suv39h set domain to act on adjacent nucleosomes to spread heterochromatin

54
Q

Where can H3K9 be observed?

A

Position Effect Varigation in Droshphilia eyes by silencing in some cells producing patches of colours

55
Q

What type of protein is Set1?

A

A trithorax protein

56
Q

Which methylation do Polycomb group proteins act on?

A

H3K27me3

57
Q

How do polycomb group proteins act?

A

PRC1 chromodomain binds H3K27me3 producing compaction

Recruits PRC2 Ezh SET to act on adjacent nucleosomes

58
Q

What does H3K27me3 do?

A

Repression by compaction into heterochromatin. Hox genes silencing and X chromosome silencing

59
Q

How is histone methylation maintained epigenetically?

A

Asf1 chaperones move Old H3/4 tetramers during replication, modifying enzymes stay attached to act on new tetramers brought by Caf1

60
Q

How much heterochromatin is maintained epigenetically?

A

75% has HP1 or PRC proteins

61
Q

Is Set a conserved sequence?

A

No

Health and Disease: Genes (6 decks)

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