Lecture 3- Epigenetic regulation of chromatin

Question 1

euchromatin

Answer 1

active genes- less dense form of chromatin

Question 2

heterochromatin

Answer 2

densely packed, inactive form of chromatin- usually exists around the edges of the nucleus

Question 3

basic chromatin structure

Answer 3

H2A, H2B, H3, H4 proteins forming a ball-like structure (histone), with approx 150nt of DNA wrapped around

Question 4

H1 proteins

Answer 4

interact with spacer DNA- is involved in the higher-order packaging of DNA

Question 5

what are epigenetic changes?

Answer 5

changes in gene/chromosome function that are mitotically stable, and do not entail a change in DNA sequence

Question 6

example of a local chromatin change involved in cellular functioning

Answer 6

CENP-A, a variation of H3, which maintains centromere function- involved in kinetochore formation, which allow chromatin binding to microtubules

Question 7

what is the histone code

Answer 7

modifications (methylation, phosphorylation, etc etc) on the N-terminal of histone proteins which can impact gene regulation

Question 8

types of protein involved in epigenetic modification

Answer 8

writers- add epigenetic marks at certain points, e.g. adding a marker to serines it sees
erasers- removing markers
readers- interact with the histone and modifications to change something about the cellular activity,

Question 9

example of epigenetic reader

Answer 9

yeast chromatin remodeling enzyme complex, RSC- helps position nucleosomes based on epigenetic signals

Question 10

example of epigenetic writer

Answer 10

JAK2- which phosphorylates a H3 and allows increased transcription of the oncogene lmo2

Question 11

example of an eraser

Answer 11

TET- demethylation- oxidise the base in DNA binding, which leads to the recruitment of DNA repair proteins to entirely replace the previously methylated base

Question 12

what does acetylation do

Answer 12

facilitates transcription by neutralising the charge on lysine and encouraging DNA to move away from these residues

Question 13

example of how modifications can keep genes active

Answer 13

NURF remodeller:
-binds to a H3, promotes nucleosome sliding
-allows TF to access the binding sequence

Question 14

example of epigenetic regulation of initiation

Answer 14

Setd2 moving along DNA with RNA polII, leading to H3 methylation, then HDACs (deacetylases) bind to these methylated histones and prevent transcription intiation

Question 15

where is DNA modified?

Answer 15

at the cytosine- usually methylation by methyltransferases

Question 16

how does DNA methylation correlate with gene activity?

Answer 16

inactive genes have higher concentrations of methylation, as methyl groups block TF binding either directly or via recruitment of inhibitory proteins by DNA methyltransferases, methyl binding domains etc

Question 17

types of signalling which can influence epigenetic modification

Answer 17

heat, chemical signalling

Question 18

how are methylated cytosines replicated?

Answer 18

-hemireplication at first- the other C is maintained, so that can act as a signal
-protein binding to hemimethylated CpG, leading to methylation of the other side

Question 19

histone marker replication

Answer 19

50% are conserved anyway, passed on from the parent cell
restoring the correct dilution requires the recruitment of protein complexes such as PRC2, which modifies new neighbouring histones joined by cohesin

Question 20

how do cells stop histone modifications going too far?

Answer 20

addition of blocking domains, which prevent incorrect modification