eukaryotic chromatin organisation

Question 1

name an example of co-activator/co-repressors.
What is their role in gene regulation?

Answer 1

Mediator, SAGA, SWI/SNF complexes act to strongly promote/repress transcription by allowing communication with TF and RNAP

Question 2

how do TF communicate with co-activators/repressors?

Answer 2

through their effector domain which interacts with proteins and able to recruit them to the DNA

Question 3

how does the CTD act with repressor/co-activators?

Answer 3

able to bind to unphosphorylated CTD and stabilise interactions between RNAP and the TF

Question 4

how do coactivators function?

Answer 4

[direct] can form a physical bridge between RNAP and TF

[indirect] can alter local chromatin structure to modulate accessibility for RNAP

Question 5

what does MNase seq- map?

Answer 5

map nucleosome positioning of genome (uses micrococcal nuclease)

Question 6

what did mnase seq inform us about distribution of eukaryotic nucleosomes?

Answer 6

precisely positioned, not random in yeast but opposite in plants

activated genes have strongly positioned nucleosome and inactive genes variable positioning

Question 7

describe nucleosome positioning in active genes?

Answer 7

chromatin is accessible so there is NFR
often flanked by strongly positioned ones

Question 8

what are DNA hypersensitivity regions

Answer 8

the peaks on DNA-seq and Atac-seq correlates with
NFR!

chromatin is accessible here

Question 9

how do nucleosomes become opened?

Answer 9

pioneer TF are able to bind to motif even if DNA is wapped around histone

able to recruit chromatin remodelling complexes to make is accessible

Question 10

what is structure of chromatin remodelling complex?

Answer 10

multi-protein ATP-ases able to drive non-covalent changes in nucleosome structure
(co-activator/repressor)

Question 11

how to chromatin remodelling complexes function?

Answer 11

slide, evict or displace, loosen histones to alter position of nucleosome

Question 12

what is ASF1?

Answer 12

a histone chaperone

Question 13

why is H2A.Z variant often found near promoter nucleosomes?

Answer 13

histones octomers with this variant are wrapped looser around DNA making it easier for elongation of transcription by RNAP to happen

Question 14

name some histone modifications

Answer 14

acetylation
methylation
phosphorylation
ubiquitilation

Question 15

why does acetylation make chromatin more accessible?

Answer 15

histones usually postive charge
acetyl neutralises this so
electostatic interactions with DNA- become weakened and loosens

Question 16

what do acetyl groups act as binding sites for?

Answer 16

binding sites for bromodomains on proteins which recognise and can spread chromatin remodelling at domain level

Question 17

how did evidence for enhanceosome structures emerge?

Answer 17

through 3C technology
‘‘chromsome confirmation capture’’ providing info about DNA interactions and spacial organisation of chromatin in cell

Question 18

how can 3C data be analysed?

Answer 18

a contact probability map is generated which frequency of interactions is displayed as a 2d heatmap

Question 19

what does 3C data basically heavily imply about DNA characteristic?

Answer 19

As there are indeed chromosomal interactions occuring, DNA is flexible to enable these interactions to occur

Question 20

what enables proximal and distal CREs to communicate with each other?

Answer 20

DNA is folded so the CREs are actually actually in close proximity to each other despite being spatially apart (on linear structure of gene body)

co-activator complexes like mediator can help with this folding

cohesins can hold 2 CREs together

Question 21

what restricts chromatin remodelling and keeps it local?

Answer 21

insulators which is a type of CRE and able to act a boundary between chromatin domains