Lecture 22 - Chromatin, Epigenetics, and the Histone Code Flashcards Preview

BIOL 200 - Molecular Biology > Lecture 22 - Chromatin, Epigenetics, and the Histone Code > Flashcards

Flashcards in Lecture 22 - Chromatin, Epigenetics, and the Histone Code Deck (40)
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1
Q

What has been used as a model organism to study transcriptional mechanism?

A

Yeast

2
Q

What are silenced regions in chromosome 3 associated with?

A

Yeast Mating Types

3
Q

What mark neutralizes the charge between histones and DNA?

A

Acetylation

4
Q

On which residues do methylations typically take place?

A

Lysine

5
Q

What does H3K4 methylation result in?

A

Activation

6
Q

What does H3K9 methylation result in?

A

Inactivation

7
Q

What process condenses the chromatin to ensure that transcription doesn’t take place?

A

Heterochromatinization

8
Q

What is dosage compensation? How is it done?

A

It is when female mammals have to shutdown one X chromosome to equalize the dose of gene expression of the X chromosome.

It is done by heterochromatinizing an X chromosome to form an inactive Barr body (highly condensed chromosome).

9
Q

What does XIST do?

A

It coats the entire X chromosome and thus shuts down most of the transcription of that chromosome.

10
Q

How is the initial choice made for which X chromosome should be turned into a Barr body?

A

There is a competition between the expression of XIST and an antisense RNA to it (TSIX).

11
Q

What histone mark ensures that the appropriate X chromosome is heterochromatinized after each cell division?

A

H3K9 Trimethylated Histones

12
Q

What is open active chromatin called?

A

Euchromatin

13
Q

Suppose you want to activate a gene downstream of a gene that is recognized by a DNA-binding domain. What must you pair with the DNA-binding domain to make this work? Why can this work?

A

You must pair it with a transcriptional activation domain from any well-characterized transcription factor.

You can do this because transcription factors are modular.

14
Q

What is a heterologous element?

A

It is a element that does not belong in the cell being tested and comes from different cells or organisms.

15
Q

Suppose you introduce a lac operator (cis-regulatory sequence) and lac repressor (lacI) joined with a strong transcriptional activation domain like VP16 into a eukaryotic cell. What will happen?

A

LacI will interact with the lacO and then VP16 will change the chromatin region in the area and activate transcription. This will co-opt the cellular apparatus to transcribe genes at very high efficiency (particularly, viral genes).

16
Q

What are SWI/SNF? What do they do?

A

SWI/SNF are chromatin remodelers that come from yeast genes.

One of the subunits of of the remodelers has homology to a helicase, but uses ATP hydrolysis to shift around the entire environment of the nucleosome which exposes regions of the DNA that would normally be hidden in the nucleosome or histone-bound high order complexes.

17
Q

Which molecular process is very important for development? Why?

A

Transcriptional regulation is very important for development because it is needed to change the transcription of each precursor cell type and eventually the fully differentiated cell types.

18
Q

What protein is often the first step in a multitude of steps that give rise to the differentiation of a lineage of cells?

A

Pioneer Transcription Factors

19
Q

What do pioneer transcription factors do?

A

They bind to a region of exposed DNA and recruit major effectors that change the chromatin configuration around the binding site.

20
Q

What is important for the termination or differentiation of an entire lineage of cells?

A

The initial chromatin change caused by pioneer transcription factors is important for this.

21
Q

Why is chromatin “looped out” to increase efficiency?

A

Chromatin gets looped out so that regions far downstream and far upstream of the gene that have to be transcribed come together, potentially linked by enhancers or other things. The outcome is that you make it advantageous for these general transcription factors to access their promoters and then transcribe their downstream genes.

22
Q

What is responsible for looping out chromatin?

A

The Mediator

23
Q

How does the mediator cause looping out?

A

The mediator mediates the interactions between upstream or downstream cis-regulatory elements, like enhancers (or UAS in yeasts). These elements bridge together and the chromatin between them forms a loop.

24
Q

Why is looping out advantageous?

A

Looping out enhances the interaction of key general transcription factors and RNA pol II with the promoters they should be interacting with and the genes they should be transcribing.

25
Q

What indirect evidence exists for looping out?

A

If you take complexes that have looped out, cut it using enzymes, and re-ligate the bits back together, you get regions of re-ligated chromatin that are thousands of bases away from eachother.

26
Q

How many major domains does the mediator have?

A

3

27
Q

Why is it often that if you eliminate key subunits of the mediator, the transcription of a class of genes will be eliminated?

A

It appears that the individual subunits interact with individual transcriptional activation domains. As such, this elimination occurs because the individual subunits confer a specificity to the mediator to interact with a class of transcription factors.

28
Q

What regions of the mediator are critical to interact with RNA pol II?

A

The Middle and Head

29
Q

How do enhancers connect to the mediator?

A

The enhancers interact with DNA-binding proteints that interact at the same time with the head of the mediator.

30
Q

Where do transcriptional activators interact with the mediator?

A

The Tail

31
Q

Why is the TATA box not actually as important as we initially thought it was?

A

It isn’t as important because transcription does not occur linearlly.

32
Q

What makes it advantageous for the general transcription factors and RNA pol II to come together so that RNA pol II can proceed from initiation to elongation?

A

The proximal binding sites and the proteins that interact with them (to activate the transcription of downstream genes) and far upstream and downstream cis-regulatory elements (enhancers) are brought together by the mediator so that the region is more advantageous to bind the general transcription factors and RNA pol II.

33
Q

What are alleles?

A

They are variants of genes on different chromosomes.

34
Q

How can two alleles respond to an enhancer at the same time?

A

Both alleles can be brought together by RNA pol II/mediator complexs in the same liquid-liquid condensate so that they can be activated at the same time.

35
Q

What are P-granules?

A

P-granules are liquids made up of RNA and proteins.

36
Q

What are P-granules important for?

A

P-granules (through phase separation, phase transition, or formation of liquid-liquid) bring together very important proteins so that they can actually carry out their function.

37
Q

How do P-granules behave (metaphorically)?

A

They behave like drop of baslsamic vinegar in oil.

38
Q

What is enhancer RNA?

A

It is RNA being made at regions in enhancers.

39
Q

What can you see if you mark the mediator with JF646 and RNA pol II with Dendra2 and then later block transcription? What does this indicate?

A

You can see that the mediator and RNA pol II are together within the cell at sites of initiation. When you block transcription, these sites go away. This indicates that the sites are dependent on transcription.

40
Q

Why may intrinsically disordered domains be critical for the liquid-liquid condensates containing the mediator and RNA pol II?

A

The elements required for transcription are found in this condensate, and since they are intrinsically disordered, a chromosome can leap into them and be activated by all of the necessary components for transcription.