Lecture 8/9 -control Of Gene Expression Pt II

Question 1

What is the mechanism for transcriptional Activation by activator proteins?

Answer 1

1. Activation by recruitment.

2. Activation by conformational change. 3. Activation by altering chromatin structure.

Question 2

Activation by recruitment

Answer 2

Activation domain interacts with one or more components Of transcriptional machinery and stabilises its binding to template DNA

Question 3

Activation by conformational change

Answer 3

Activation domain induces a conformational change in a component of the basal transcriptional machinery to stimulate RNA polymerase II to initiate transcription

Question 4

Activation by altering chromatin structure

Answer 4

Activation domain recruits chromatin remodelling/modifying proteins (co-activators) to modulate chromatin structure around promoters

Question 5

What are the transcriptional factor activation domains?

Answer 5

Acidic region.

Glutamate rich regions Proline rich regions

Question 6

What factors contains acidic regions?

Answer 6

Yeast GCN4 GAL4.
Nuclear receptors

Question 7

What factors contains Glutamate-rich regions?

Answer 7

SP1, Oct1,Oct2, AP2

Question 8

Which factors contain proline rich regions ?

Answer 8

CTF/NF1 AP2 c-jun Oct2

Question 9

What are the other roles of activation by recruitment?

Answer 9

Increases binding of a particular component of the basal machinery so enhancing its assembly Activator alters confirmation of an already bound factor so stimulating the activity/or stability of the complex

Question 10

Activators can interact with TFIID

Answer 10

Enhances binding of TFIID to TATA box, improving rate of PIC complex Alter the confirmation of TFIID stimulating its activity by increasing its ability to recruit other PIC components or by enhancing ability to stimulate transcription.
Interaction is through TBP or one or more of TAFs

Question 11

Activators can interact with TFIID via TAFs

Answer 11

Different activators target different TAFs.

Different cell types can have cell type-specific TAFs

Question 12

What are TAFs a critical intermediary of?

Answer 12

Between activators and basal transcription complex

Question 13

Activators can interact with TFIIB

Answer 13

Stimulation of assembly of PIC/activity of basal transcriptional complex after TFIID has bound

Question 14

Who do TFIIB interact with ?

Answer 14

Acidic activators

Question 15

What do CTD of RNA pol II interact with?

Answer 15

Mediator complex

Question 16

Why is the interaction between CTD and mediator important?

Answer 16

Required for the response to transcriptional activators

Question 17

What do mediator form?

Answer 17

molecular bridge between activators and RNA pol II

Question 18

How many subunits does the mediator complex have?

Answer 18

30’subunit

Question 19

How many sub complexes does the mediator complex have?

Answer 19

3

Question 20

What are the three sub complexes of mediator complex?

Answer 20

Head, middle and Tail

Question 21

What does the head of the mediator complex interact with?

Answer 21

RNA pol II CTD

Question 22

What does the tail of the mediator complex interact with?

Answer 22

Activators

Question 23

What do different classes of activators interact with ?

Answer 23

Different mediator subunits

Question 24

Mediator interacts with activator proteins and what else?

Answer 24

Pol II transcription machinery

Question 25

What is the principle that governs the function of all activators?

Answer 25

DNA binding domain determines specified for the target promoter enhancer

Question 26

What is the DNA binding domain responsible for?

Answer 26

Localising a transcription-activating domain in the proximity of the basal apparatus

Question 27

What is the structure of an Activator that works directly?

Answer 27

DNA binding domain and an activating domain within same protein that affects transcription directly

Question 28

What happens when an Activator does not have an activating domain?

Answer 28

Work by binding a co-Activator that has activating domain (interaction between 2 distinct proteins)

Question 29

What does co-Activator do?

Answer 29

Does not bind DNA itself Interacts with a DNA-bound transcriptional activator to transmit the signal to the basal transcription complex

Question 30

What is an example of co-Activator?

Answer 30

CREB-binding protein (CBP/p300) which is recruited to DNA by the DNA-binding transcription factor partner, CREB

Question 31

What does CREB-binding protein (CBP/p300) mediate?

Answer 31

Transcriptional activation via a number of other DNA-binding transcription factors partners involved in a variety of signalling pathways

Question 32

What is CREB-binding protein (CBP)?

Answer 32

Histone Lysine acetyltransferase

Question 33

What acts upon CBP/p300?

Answer 33

CREB. Steroid/thyroid hormone receptors STATs NF-KB AP1. SREBP MyoD P53

Question 34

CREB

Answer 34

Cyclic AMP

Question 35

Steroid/thyroid hormone receptors

Answer 35

Steroid/thyroid hormone

Question 36

STATs

Answer 36

Interferon/cytokines

Question 37

NF-KB

Answer 37

Inflammation

Question 38

AP1

Answer 38

Growth stimulation

Question 39

SREBP

Answer 39

Cholesterol

Question 40

MyoD

Answer 40

Muscle differentiation

Question 41

P53

Answer 41

Growth arrest

Question 42

Histone Lysine acetyltransferase

Answer 42

Recruited by a variety of separate DNA-binding partners (activators) to activate transcription Mediate transcriptional activation by changing chromatin structure directly (charge) or indirectly (recruitment of acetyl-Lysine binding proteins) Allows access fo DNA and transcriptional start sites by opening up chromatin

Question 43

What is Lysine (K) acetyltransferase (KAT)?

Answer 43

Enzyme present in large complexes that acetylates Lysine residues in histonnes

Question 44

Where are HAT recruited to?

Answer 44

Recruited to promoters as co-activators by transcriptional activators Activator transcription from promoter; opening up/loosening chromatin is by recruitment of basal transcriptional machinery

Question 45

What is GCN4?

Answer 45

Transcriptional activator that binds to upstream activating sequence (UAS) though DNA-binding domain

Question 46

What does GCN4 activation domain interact with?

Answer 46

Multi-protein GCN5 HAT complex (co-Activator)

Question 47

What does GCN4 allow?

Answer 47

Access of PIC to DNA and transcriptional start site

Question 48

Transcriptional effect of acetylation of Lysine

Answer 48

Activation

Question 49

Transcriptional effect of methylation is Lysine at H3; 4,36 and 79

Answer 49

Activation

Question 50

Transcriptional effect of methylation of Lysine at H3;9,27 and H4 position 12,20

Answer 50

Repression

Question 51

Transcriptional effect of methylation at arginine

Answer 51

Activation

Question 52

transcriptional effect of ubiquilated Lysine at H2B position 120

Answer 52

Activation

Question 53

Transcriptional effect of ubiquilated Lysine at H2A position 119

Answer 53

Repression

Question 54

Transcriptional effect of sumoylated Lysine

Answer 54

Repression

Question 55

transcriptional effect of phosphorylated serine/threonine

Answer 55

Activation

Question 56

What recognises acetyl lysines?

Answer 56

A family of binding proteins containing bromodomains

Question 57

TAFII250

Answer 57

Part of TFIID and therefore transcription is promoted by recruitment of the PIC

Question 58

What can remodel chromatin?

Answer 58

Transcriptional activators

Question 59

What can acetylation of histones do?

Answer 59

Weakens/loosens nucleosome which can: Facilitate access of an Activator to DNA Recruitment of activators tang recognise and bind to acetyl-Lysine Promote nucleosome displacement from promoter in an energy-dependent process

Question 60

What is chromatin remodelling?

Answer 60

The energy-displacement or re-organisation of nucleosomes that occurs in conjugation with activation of genes for transcription

Question 61

What does all remodelling complexes contain?

Answer 61

Related ATPase catalytic subunit

Question 62

What can remodelling complexes do?

Answer 62

Alter, slide or displace nucleosomes

Question 63

What can some remodelling complexes exchange?

Answer 63

One Histone for another in a nucleosome

Question 64

What does transcriptional activation involve?

Answer 64

Multiple changes to chromatin

Question 65

What is transcriptional activation?

Answer 65

Synergistic

Question 66

What are the mechanisms of action of Transcriptional Repressors?

Answer 66

Prevent an Activator binding through chromatin structure Overlapping binding sites Repressor sequesters the Activator Repressor quenches the transcriptional Activation ability of the Activator Repressor degrades Activator Directly Repress transcription

Question 67

Transcriptional Repression through chromatin structure

Answer 67

Establish repressive/tightly packed chromatin (heterochromatin) around proteins

Question 68

What is Histone deacetylase (HDAC)?

Answer 68

Enzyme that removes acetyl groups from histones; May be associated with repressors of transcription

Question 69

Where are deacetylases present?

Answer 69

Complexes with repressor activity

Question 70

What can Repressors interact with?

Answer 70

Co-Repressors

Question 71

What is UME6?

Answer 71

Transcriptional repressor that binds to upstream repressor sequence (URS1)

Question 72

What does UME6 interact with?

Answer 72

Separate multi-protein SIN3 complex that includes RPD3 Histone deacetylase

Question 73

What is Methylation catalysed by?

Answer 73

Histone methyltransferase (KMTs)

Question 74

Readers of Lysine methylation

Answer 74

Methyl-lysines are recognised by a family of binding proteins containing chromodomain

Question 75

HP1

Answer 75

Heterochromatin assembly Transcriptional silencing

Question 76

Where does HP1 bind to?

Answer 76

Methyl-Lysine on Histone H3 Lysine 9 through its chromodomain

Question 77

During early embryogenesis what do Repressors associate with?

Answer 77

PRC2 co-repressor complex

Question 78

What does PRC1 complex bind to?

Answer 78

Methylated Lysine 27 and further condenses chromatin into inactive form

Question 79

How is Repression maintained?

Answer 79

Absence of the original repressor throughout adult development - transcriptional memory

Question 80

What do Lysine methylation and acetylation do?

Answer 80

Cross talk e.g. H3K9

Question 81

What can Lysine be?

Answer 81

acetylated or methylated

Question 82

How can processes such as transcription be regulated?

Answer 82

Switching modifications

Question 83

What do Repressor bind to?

Answer 83

specific DNA sequence preventing/blocking the action of the Activator (A)

Question 84

What is a repressor which ubiquitinate the P53 Activator and promote degradation by proteases?

Answer 84

MDM2

Question 85

What is a repressor that is itself a protease and degrades the Activator directly ?

Answer 85

AEBP1

Question 86

What is Dr1 factor?

Answer 86

bind TBP preventing binding of TFIIB and therefore assembly of the PIC

Question 87

What displaces TBP from DNA?

Answer 87

Mot1