L2 - How are promoters selected?

Question 1

How is DNA packaged?

Answer 1

146 bp of DNA wraps round histone forming nucleosomes

Question 2

What feature do some promoters have to keep txn?

Answer 2

Sequences that discourage nucleosome occupancy

Question 3

How is txn inhbited?

Answer 3

methylation at the CpG

Question 4

What is the cpG

Answer 4

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

Question 5

What happens when CpG is unmethylated?

Answer 5

Recruits TFs such as CFP1 and MLL family

Question 6

What do CFP1 and MLL do?

Answer 6

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

Question 7

What do H3K4Me3’s do?

Answer 7

Trimethlate lysine 4 of histone H3

Question 8

What can mutations in MLL cause?

Answer 8

Aggressive leukaemias resulting from fusion proteins misregulating target genes

Question 9

What recognises H3K4me3 and what does it do?

Answer 9

Chromatin remodeller (CHD1)
Helps move nucleosomes away from promoter

Question 10

What subunit of TFIID also recognises H3K4me3?

Answer 10

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

Question 11

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

Answer 11

Pull down assays with beads

Question 12

What is ChIP and what is used for?

Answer 12

Chromatin immunoprecipitation

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

Question 13

What parts of TFIID contribute to promoter recognition?

Answer 13

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

Question 14

Why is there so many sites of contact for TFIID?

Answer 14

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

Question 15

How do TFs help initation?

Answer 15

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

Very inefficient with out help

Question 16

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

Answer 16

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

Question 17

What do activating TFs also do?

Answer 17

Recruit chromatin remodellers and histone modifiers

Question 18

What does p53 recruit other than TFIID?

Answer 18

p300 histone acetyltransferase (HAT)

Question 19

What does HAT do

Answer 19

acetylates histone H4 so it is recognised by TAF1

Question 20

What are LOF mutations in chromatin remodellers associated with and exmaple

Answer 20

Various cancers

SNF5 deletions in malignant rhabdoid tumours

Question 21

What did ChIP-PCR show about histone H4?

Answer 21

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

Question 22

What are the erasers of acetylation on histones?

Answer 22

HDACs (histone deacetylases)

Question 23

What recognises acetylated histones?

Answer 23

Bromodomains

Question 24

What does TAF1 having 2 bromodomains do?

Answer 24

Allows simultaneous recognition of two close acetylated lysines giving enhanced specificity

Question 25

What can be used to treat cancers?

Answer 25

HDAC inhibitors to reactive silenced genes

Question 26

What is an example of an HDAC inhibitor

Answer 26

SAHA

Question 27

what do activating TFs also recruit?

Answer 27

Basal TFs directly and indirectly

Question 28

What can pioneer TFs do? examples

Answer 28

Bind nucleosomal DNA and increase accessibility | e.g. FOXA1, AP1

Question 29

What does binding of AP1 to DNA do?

Answer 29

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

Question 30

What is interesting about FOXA1 and what does it allow?

Answer 30

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

Question 31

How is FOXA1 implicated in breast cancer?

Answer 31

Overexpress ER, tumour growth is hormone sensitive | FOXA1 or AP1 may redirect ER to alternative gene targets increasing severity

Question 32

What are the features of enhancerS?

Answer 32

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)

Question 33

What is chromosome conformation capture use for?

Answer 33

Test interactions between regions of DNA in cells

Question 34

What feature do enhancers have?

Answer 34

Cell type selective

Question 35

How are chromatin loops stabilised?

Answer 35

Cohesin and mediator

Question 36

What are the features of cohesion?

Answer 36

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

Question 37

What are the features of the mediator?

Answer 37

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