L5

Question 1

TFs

Transcription factors

Answer 1

TFs can be repressors or activators (de/increase transcription driven by basal machinery)

Intrinsic signals

Question 2

Master regulator

Answer 2

Coordinates expression of multiple genes through TFs, drives entire transcription programme to establish fate

Question 3

Extrinsic signals

Answer 3

Coordinate intercellular pathways that regulate the Maste Regulators

Question 4

Competition that determines cell fate

Answer 4

4 major pathways pushing for cells to reach major germline fates; each morphogen leads to expression of key gene(s) that code for a master TF; morphogens also lead to activation of feedback TFs (auto/paracrine feedback which can be +ve/-ve (fate promoting/ stalling)); each pathway trying to increase master TF to above autoregulation threshold (point at which this is reached determined by morphogen concentration and duration of exposure)

Question 5

Endoderm pathway

Morphogen -> receptor -> 2nd messenger -> key TF genes -> cell fate

Answer 5

Veg1 [Activin, Nodal] -> Alk4/7 -> Smad 2/3 -> Gata4/6 [Sox17, FoxA2] -> Endoderm

Question 6

Mesoendoderm pathway

Morphogen -> receptor -> 2nd messenger -> key TF genes -> cell fate

Answer 6

Veg1 [Activin, Nodal] -> Alk4/7 -> Smad 2/3 -> Gata4/6 [Brach] -> Mesoendoderm

Question 7

Mesoderm pathway

Morphogen -> receptor -> 2nd messenger -> key TF genes -> cell fate

Answer 7

TGFβ -> Alk5 -> Smad2/3 -> Gata4/6 [Brach, Twist/Snail] -> Mesoderm

Question 8

Ectoderm pathway

Morphogen -> receptor -> 2nd messenger -> key TF genes -> cell fate

Answer 8

BMP4 -> BADR1/2 -> Smad1/5/8 -> Gata2/4 [MSX1] -> Ectoderm

Question 9

Neuroectoderm pathway

Morphogen -> receptor -> 2nd messenger -> key TF genes -> cell fate

Answer 9

FGF4/8 -> FGFR -> MAPK -> Oct4, Sox2 -> Neuroectoderm

Question 10

Alternative mesoderm pathway

Morphogen -> receptor -> 2nd messenger -> key TF genes -> cell fate

Answer 10

WNT8 -> FRZ:2RP5/6 -> β Catenin -> Brach [Twist/Snail/Slug] -> Mesoderm

Question 11

Which of the 4 starter molecules in the major pathways are part of the TGFβ superfamily?

Answer 11

Veg1, TGFβ

Question 12

What determines broad fates?

Answer 12

Gradient of each pathway

Question 13

What determines sub-fates?

Answer 13

Concentration dependent effect of gradients on genes

Question 14

Can cells establish new fates as they mature?

Answer 14

Yes, if a gradient is generated in an area form which it was previously absent (depends on cell competency as well)

Question 15

How do gradients work?

Answer 15

Single TF can generate multiple cell types in a concentration dependent manner; possible when TF has different affinity for different genes (at low conc may only bind high affinity, at high, best targets now saturated and can bind targets with weaker affinity); morphogen provides gradient and this determines what concentration of corresponding master TF will be activated in each cell

This how single TF can generate multiple cell types in a group of cells that were previously homogenous

Question 16

How do lower affinity genes get expressed at high morphogen concentrations to ensure none others do?

Answer 16

Lower affinity genes usually activate a gene/factor that inhibits higher affinity genes

Question 17

Two mechanisms by which master TFs can signal to target genes:

Answer 17

Digital- all or nothing
Analogue- where divergent affinity ends are activated give cell different sub fates of gene X
Could be one TF doing both or one TF could generate secondary TFs, one of which is analogue and one of which is digital

Question 18

In general, how do transcription cascades work?

Answer 18

Master TF digitally specifies fate X, same TF may then specify sub fates X1, X2, X3 in a graded (analogue) fashion

Question 19

How are alternative fates of border cells created?

Answer 19

Gradients usually work in competing pairs, leaving the cells at the crossover between separate gradients unique

Question 20

Function of border cells?

Answer 20

Interaction between border cells often leads to up regulation of another morphogen which can then establish a new morphogen sub gradient for sub patterning

Question 21

Two additional signalling pathways which are critical for neural tube patterning are

Answer 21

SHH (transmembrane receptor mechanism) and RA (nuclear hormone receptor mechanism)

Critical due to their ability to generate gradient based sub fates

SHH important in ventral patterning, RA important in hindbrain patterning

Question 22

SHH pathway

Answer 22

SHH -> Patched (R) -> Gli3 (2nd messenger/gradTF) -> Complex Homeobox Factors e.g. Pax (Master TF)

Question 23

RA pathway

Answer 23

RA -> RAR (cytoplasmic R) -(nucleus)-> Simple Homeobox Factors e.g. Hoxb