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Eukaryotic Gene Expression > L2 - How are promoters selected? > Flashcards

L2 - How are promoters selected? Flashcards

1
Q

How is DNA packaged?

A

146 bp of DNA wraps round histone forming nucleosomes

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2
Q

What feature do some promoters have to keep txn?

A

Sequences that discourage nucleosome occupancy

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3
Q

How is txn inhbited?

A

methylation at the CpG

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4
Q

What is the cpG

A

Regions enriched for CG dinucleotides (CpG islands) with promoters in

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5
Q

What happens when CpG is unmethylated?

A

Recruits TFs such as CFP1 and MLL family

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6
Q

What do CFP1 and MLL do?

A

Recruit H3K4 methyltransferase complexes and allow it to spread to adjacent nucelosomes

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7
Q

What do H3K4Me3’s do?

A

Trimethlate lysine 4 of histone H3

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8
Q

What can mutations in MLL cause?

A

Aggressive leukaemias resulting from fusion proteins misregulating target genes

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9
Q

What recognises H3K4me3 and what does it do?

A 
Chromatin remodeller (CHD1)
Helps move nucleosomes away from promoter
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10
Q

What subunit of TFIID also recognises H3K4me3?

A

Complex of TBP with 13 TAFs (TBP associated factor) (TAF3 binds H3k4me3)

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11
Q

How was it found which proteins and subunits bind to each other?

A

Pull down assays with beads

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12
Q

What is ChIP and what is used for?

A

Chromatin immunoprecipitation

To test which regions of DNA are bound by a protein in cells

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13
Q

What parts of TFIID contribute to promoter recognition?

A

TAF1 - binds histone H4 and initiator (Inr) DNA
TAF6 - binds downstream promoter element (DPE)
TBP binds TATA box

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14
Q

Why is there so many sites of contact for TFIID?

A

Provides versatility for different promoter arrangments (TATA-less promoters)

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15
Q

How do TFs help initation?

A

Assist in recruitment of TFIID, basal factors and pol 2.

Very inefficient with out help

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16
Q

What is an example TF helping in recruitment at pol 2?

A

Sp1 binds g/c rich sites in DNA of many promoters and recruits TFIID with TAFs

17
Q

What do activating TFs also do?

A

Recruit chromatin remodellers and histone modifiers

18
Q

What does p53 recruit other than TFIID?

A

p300 histone acetyltransferase (HAT)

19
Q

What does HAT do

A

acetylates histone H4 so it is recognised by TAF1

20
Q

What are LOF mutations in chromatin remodellers associated with and exmaple

A

Various cancers

SNF5 deletions in malignant rhabdoid tumours

21
Q

What did ChIP-PCR show about histone H4?

A

Levels incease when p53 and p300 bind a gene induced by UV irradiation

22
Q

What are the erasers of acetylation on histones?

A

HDACs (histone deacetylases)

23
Q

What recognises acetylated histones?

A

Bromodomains

24
Q

What does TAF1 having 2 bromodomains do?

A

Allows simultaneous recognition of two close acetylated lysines giving enhanced specificity

25
Q

What can be used to treat cancers?

A

HDAC inhibitors to reactive silenced genes

26
Q

What is an example of an HDAC inhibitor

A

SAHA

27
Q

what do activating TFs also recruit?

A

Basal TFs directly and indirectly

28
Q

What can pioneer TFs do? examples

A

Bind nucleosomal DNA and increase accessibility

e.g. FOXA1, AP1

29
Q

What does binding of AP1 to DNA do?

A

Allows access of glucocorticoid receptor to adjacent site - allowing cooperative binding of other TFs

30
Q

What is interesting about FOXA1 and what does it allow?

A

DNA binding domain resembles linker histones
Allows oestrogen receptor (ER) to access DNA
Binds enhancers, not promoters

31
Q

How is FOXA1 implicated in breast cancer?

A

Overexpress ER, tumour growth is hormone sensitive

FOXA1 or AP1 may redirect ER to alternative gene targets increasing severity

32
Q

What are the features of enhancerS?

A

Clusters of TF binding sites
1m in human genome
Can be 100s of kb from gene
Marked by histone acetylation, DNase hypersensivity and H3K4me1 (different from 3)

33
Q

What is chromosome conformation capture use for?

A

Test interactions between regions of DNA in cells

34
Q

What feature do enhancers have?

A

Cell type selective

35
Q

How are chromatin loops stabilised?

A

Cohesin and mediator

36
Q

What are the features of cohesion?

A

Rig shaped to accommodate 2 strands
Stabilise interactions between enhancer and promoter
Mutations result in developmental defects (retardation)

37
Q

What are the features of the mediator?

A

26 subunits
Binds unphos CTD of pol 2
Target for many activators
Mutations result in developmental and neurological disorders

Eukaryotic Gene Expression (8 decks)

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