Discussion Paper 5 Flashcards

You may prefer our related Brainscape-certified flashcards:
1
Q

Enhancer regions of genes contain binding sites for…

A

Transcription factors which are cell or tissue-specific

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

True or false: basal promoter regions contain binding sites for cell-specific TFs

A

False - not necessarily but some do. Most promoter regions have binding sites for more general TFs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Which retinal cells tend to continue to develop/be born postnatally?

A

Rods, bipolar cells, muller glia

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Most of the retinal development focussed on in this paper occurs (pre-natally/post-natally)

A

Postnatally

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What cell fate decision is being examined in this paper?

A

Rod vs Bipolar cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

As determined by previous studies, what occurs when Blimp1 (a transcription factor) is knocked out?

A

There is a loss of photoreceptors and a gain in bipolar cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is the underlying big picture question of this paper?

A

How does a GRN affect the bipolar cell vs rod cell fate decision?

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is the underlying question of figure 1A?

A

What are the elements which regulate Blimp1?

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the significance of sequence conservation in figure 1A?

A

Conservation is a good indicator that that region of the gene has some essential role - especially looking for non-coding regions with high conservation = good sign of regulatory element

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the experimental approach used to address the question in figure 1A?

A

“Promoter bashing”: chop the promoter region into bits to see which parts are essential for driving expression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the most important finding of 1c?

A

Using the 12kb region identified in figure 1A is sufficient to direct transcription of EGFP to the retina

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What was the main technique used in this study to determine if constructs were directing expression to the retina?

A

In vivo electroporation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the model organism used in this study?

A

Mice

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Why did the authors co-electroporate with CAG-LacZ?

A

This is a control to make sure the electroporation was working - LacZ = the dye, CAG = ubiquitous promoter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How long is a typical enhancer?

A

<500bp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is being demonstrated by figures 1b and 1c?

A

Breaking up the 12kb region into smaller bits to find the necessary sequence which is required for retinal-specific targeting - identify a 108bp region which is sufficient and necessary to direct expression to the retina

17
Q

What are the underlying questions of figure 2E-K? (2)

A
  1. What is the fate of the cells which are endogenously driven by the B108 enhancer?
  2. When does the B108 enhancer turn on?
18
Q

Describe the experimental approach used to address the question in figure 2e-k

A

Fate mapping using cre-lox system to examine the fate of cells that express B108 (when cre present under promoter preceding cre, will cleave cells and turn on egfp)

19
Q

Describe the most important findings of figure 2e-k

A

Most of the cells with the B108 promoter are rod cells - b108 sufficient to illuminate the photoreceptor cells

20
Q

What conclusions can be made about the cells that express B108-Cre?

A

The B108 enhancer directs expression to postmitotic photoreceptors

21
Q

If B108 was expressed in progenitor cells, what would we see in this figure?

A

Bipolar cells would also be expressing EGFP - because we know they go through a cell fate decision

22
Q

What data in the paper supports the fact that B108-expressing cells are postmitotic?

A

Did EdU labelling: EdU labels cells which are replicating, and there were no EdU and B108-GFP+ cells

23
Q

What is the underlying question of figure 3?

A

Is B108 required for PR development?

24
Q

What is the experimental approach used to determine the requirement of the B108 enhancer?

A

Used CRISPR to remove the B108 promoter, then use cre-lox system to mark PR cells which have switched fate to BP in the absence of the B108 promoter, or mark BPs