lecture 4

Question 1

post translational modifications of histones

Answer 1

acetylation and methylation

Question 2

the histone code

Answer 2

types and arrangement of modifications on the N terminal tail are a code that tells you what the transcriptional state of the underlying DNA is

Question 3

enzymes such as HATs _____ the code

Answer 3

write

Question 4

enzymes such as histone deacetylases _____ the code

Answer 4

erase

Question 5

proteins such as bromodomain proteins ____ the code

Answer 5

read and bind to acetyl lysines

Question 6

chromodomains proteins and PWWP proteins bind to

Answer 6

methyl lysines

Question 7

ATP dependent chromatin remodelers, they

Answer 7

use ATP from ATP hydrolysis to change the structure of chromatin

Question 8

there are 4 different families of the chromatin remodelers

Answer 8

SWI2/SNF2, ISWI, CHD/Mi2 and Ino80

Question 9

the families are characterised by

Answer 9

additional domains and structure of the ATPase domain

Question 10

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

Answer 10

slide nucleosomes along DNA, unwrapping of DNA from the nucleosome, remove nucleosome, spacing of nucleosomes and exchange histones for histone variants

Question 11

the catalytic subunit SWI/SNF is called Snf2 ir Swi2

Answer 11

it hydrolysis 1000 ATP molecules per min in the presence of DNA or nucleosomes

Question 12

Snf2 is related to

Answer 12

DNA helicases

Question 13

Snf2 is though to be a molecular motor that uses the energy from

Answer 13

ATP hydrolysis to track along side DNA and induce torsion which introduces loops and change in structure, results in disruption of histone DNA interactions and movement o the nucleosome

Question 14

they change the position of DNA around the nucleosome

Answer 14

makes potential binding sites accessible

Question 15

bromodomains in Snf2 help tether it to acetylated nucleosomes

Question 16

human SWI?SNF (hBRM and BRG1) are very similar to the

Answer 16

yeast SWI/SNF

Question 17

SWI/SNF mutations can causes

Answer 17

cancer as they are tumor suppressors

Question 18

transcription repression by recruiting chromatin modifying factors eg

Answer 18

histone deacetylases (HDACs), ATP-dependent remodelers and histone methylases

Question 19

histone deacetylases

Answer 19

repressed regions are hypoacetylated (low)
mediated by HDACs
4 major groups of HDACs: class I, II and IV (classical HDACs dependent of zinc in their active site). class III is SIr2 family (use NAD as a co factor)

Question 20

HDACs commonly function in

Answer 20

large multi subunit complexes eg SIN3 co repressor

Question 21

URS (upstream repressing sequence) is bound to by

Answer 21

DNA binding domain, then Ume6 brings the HDAC complex to chromatin. Rpd3 (the catalytic subunit) then deacetylates the lysines from the histone tails

Question 22

co repressor as it doesn’t bind to DNA directly

Question 23

some ATP dependent remodelers mediate transcriptional repression

Answer 23

eg the NuRD complex which belongs to the Mi2/CHD family

Question 24

the NuRD complex plays roles in

Answer 24

normal differentiation and tumourogenesis (supressed the transcription of tumour supressor genes)

Question 25

NuRD cause the chromatin to be more

Answer 25

tight and very regularly, causes a closed chromatin structure turning transcription off

Question 26

not all ATP dependent remodeling complexes are used for

Answer 26

increasing transcription

Question 27

heterochromatin

Answer 27

there are 2 types of chromatin: euchromatin and heterochromatin
euchromatin is gene rich and has the potential to be transcribed
heterochromatin is gene poor, contains repetitive regions and associated with transcriptional silencing

Question 28

heterochromatin is found at

Answer 28

centromeres and telomeres

Question 29

features of heterochromatin

Answer 29

hypoacetylation, specific histone H3 methylation (eg Lys9 + Lys27) and association of specific silencing factors

Question 30

assembly of H3Lys9me):
in order for a lysine to be methylated it must be

Answer 30

deacetylated

Question 31

HDACs remove the

Answer 31

acetyl group

Question 32

methylation of Lys9 on histone H3 is mediated by

Answer 32

suvar39

Question 33

methyl is recognised by

Answer 33

HP1 (heterochromatin protein 1)

Question 33

methyl is recognised by

Answer 33

HP1 (heterochromatin protein 1)

Question 34

heterochromatin protein 1is a

Answer 34

chromodomain protein

Question 35

chromodomains often recognise and bind to

Answer 35

methylated lysine residues

Question 36

the chromodomains of HP1 is specific for

Answer 36

H3 Lys9me2/3 (di(2) or tri(3) methylated)

Question 37

HP1 interacts with itself to bring adjecent nucleosomes close together to form

Answer 37

compact nucleosomal arrays

Question 38

acts as an interaction platform for the recruitment of further activities that prevent recruitment/activity of

Answer 38

RNA pol II

Question 39

reporter silencing assays

Answer 39

ade6 gene is in euchromatin and being expressed
when ade6 gene is expressed cells can make their own adenine and colonies are white

ade6 gene was deleted at normal location and was put in the middle of heterochromatin. HP1 will assemble over the ade6 gene so it can no longer be expressed. the cells is the colonies now are red

mutate a gene in heterochromatin then the colonies are white/pink