lecture 4 recap

Question 1

whats the histone code

Answer 1

types of modifications on the N terminal tail that tells you what the transcriptional state of the DNA is

Question 2

chromodomains and PWWP proteins bind to

Answer 2

methylated lysines

Question 3

how do ATP dependent chromatin remodelers change the structure of chromatin

Answer 3

use energy from ATP hydrolysis

Question 4

what are the 4 different families of the ATP chromatin remodelers

Answer 4

SWI2/SNF2, ISWI, CHD/Mi2 and Ino80

Question 5

the can use the energy from ATP hydrolysis to do one or more of these reactions

Answer 5

1. slide nucleosomes along DNA
2. unwrapping DNA from the nucleosome
3. remove nucleosome
4. spacing of nucleosomes
   5.exchange histones for histone variants

Question 6

the catalytic subunit of SWI/SNF is

Answer 6

Snf2 or Swi2

Question 7

Snf2 uses energy from ATP hydrolysis to induce what

Answer 7

torsion which results in disruption of histone-DNA interactins and movement of the nucleosome

Question 8

they change the position of the DNA around the nucleosome which makes what

Answer 8

potential binding sites accessible

Question 9

what in the Snf2 help tether it to the acetylated nucleosomes

Answer 9

bromodomains

Question 10

what can ATP- dependant complexes co operate with

Answer 10

HATs

Question 11

HDACs commonly function in large multi subunit complexes for example

Answer 11

SIN3 co repressor

Question 12

how HDACs work:
URS is bound to by

Answer 12

DNA binding domain on Ume6 (repressor protein)

Question 13

Ume6 binds to HDAC complex and brings it to the chromatin. what subunit in the HDAC deacetylates the lysines?

Answer 13

Rpd3

Question 14

what are co-repressors

Answer 14

repressors that dont bind to DNA directly

Question 15

what family of ATP dependent remodellers does NuRD complex belong to

Answer 15

Mi2/CHD family

Question 16

NuRD cause the chromatin to be more

Answer 16

tight and causes a closed chromatin structure turning transcription off

Question 17

what the the two types of chromatin

Answer 17

heterochromatin and euchromatin

Question 18

euchromatin is

Answer 18

gene rich and has the potential to be transcribed

Question 19

heterochromati is

Answer 19

gene poor, contains repetitive regions and associated with transcriptional silencing

Question 20

where is hetermochromatin found

Answer 20

at centromeres and telomeres

Question 21

heterochromatin has specific methylation of what

Answer 21

H3 (Lys9 and Lys27)

Question 22

assembly of H3Lys9me
in order for a lysine to be methylated it bust be

Answer 22

deacetylated

Question 23

what removes that acetyl group

Answer 23

HDACs

Question 24

methylation of Lys9 on histone H3 is mediated by

Answer 24

suvar39

Question 25

methyl on Lys9 is recognised by

Answer 25

HP1 (heterochromatin protein 1)

Question 26

HP1 is a

Answer 26

chromodomain proteins

Question 27

HP1 binding to methylated H3Lys9 is thought to do what

Answer 27

compact nucleosomal arrays by interacting with itself

Question 28

HP1 also acts as an interation platform for what

Answer 28

further activities that prevent recruitment and activity of RNA pol II