W4L2 combinatorial transcription control

Question 1

What can DBD protein do and Regulatory protein in the Gal pathway

Answer 1

! DnaBindingDomain proteins can recruit proteins for repression as well as activation
! Glucose represses GAL gene expression
-Gulcose lead to Mig1 site binding, leading to Tup1- Ssn6 co-repressor (1 tup1 per 4 ssn6)
-this make the chromatin repressive, prevent Gal4 activation

Question 2

synergy between activators

Answer 2

—This apply to either binding of DNA as well as activation of transcription by recruitment of RNA
For example: there are two regulation site, 1 binding lead to 1 unit of transcription and binding of 2 lead to 2 unit of transcription
When both are bind, it lead to a much higher level of transcription

Question 3

Negative control mechanism

Answer 3

-two transcription factor can interact which can lead to:
-masking of the acitivation surface
-competitive DNA binding (this is based on affinity which can change)
-direct interaction with the GTF, recruitment of a negative corepressor

Question 4

Mating locus of C.ser

Answer 4

• on the 3rd chromosome, have 2 different gene on the allele MATa and MATalpha
  -both share the region W,X and Z. Only different in Y, separate into Ya and Yalpha
  -change type by changing the Y area

Question 5

Nearby structure of MAT

Answer 5

-on the right is always HMRa which contain X,Ya and Z
-on the left is W,X,Yalpha and Z
-these two flanking loci are blocked from being express, only MAT is allow
-Used to copy information in to the MAT gene

Question 6

How does mother cell change mating type in S.cer

Answer 6

-copy the information from either the left or right fragment through a specialised procedure
- there is repressive chromatin that block transcibtion but does not block recombination/ gene conversion
-they are repressed by SIR gene )1-4)

Question 7

Fuction of SIR gene

Answer 7

Sir1 – Nucleator function
Sir2 – HDAC, Surtuin family
Sir3 – BAH domain, Orc1 diverged
Sir4 – Sir2/3/4 scaffold

Question 8

SIR gene in action

Answer 8

• silencer E (essential) is needed to recruit sir on W and X
  -silencer I (important): increase the efficiency of SIR recruitment on Z
  In HMR: ORC, Rap1 and Abf bind to E site while Abf1 and ORC bind to I
  In HML: Rap1,ORC and Sum 1 bind to E while Abf, Rap1 and ORC bind to HML

Question 9

Fuction of MATal and MATa gene

Answer 9

-MATal contain al1 and al2
-al2 is a repressor which block a specific gene expression(constitutively)
-al1 activate al specific gene
-RME prevent diploid specific gene to be repressed
-In MATa gene, a specific they are expressed constitutively so no need to do anything

Question 10

Mat gene in diploid state

Answer 10

-both MATa and MATal is expressed
-a1 and al2 form a dimmer, blocking HO and RME. This allow expression of diploid specific gene
-the dimer also block the expression of al1 which activate al specific gene

Question 11

Expression of mat gene in different condition

Answer 11

Question 12

Yeast respond to mating hormone

Answer 12

-in transcription factor contain TUP1, SSN6, STE12 and MCM1 (for DNA binding)
-when a pheromone is detected, it lead to STE12 phosprylisation
-in a cell, STE12 and MCM1 bind to the a-specific gene -> constitutive
-in al cell, a1 need to bind to the DNA so the al specific gene inductable. Al2 bind to the binding site in a-specific gene, recruit TUP1 SSN6 corepressor to prevent fuction

Question 13

yeast DNA binding in diploid state

Answer 13

-a1 and al2 both bind to repressor, recruit SSN6 and TUP1 corepressor, turning haploid specific gene off
-al2 then act on the a-specific gene to turn it off