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MCB2050 Part 1 > Chromatin and Molecular Mechanisms of Transcription Repression and Activation > Flashcards

Chromatin and Molecular Mechanisms of Transcription Repression and Activation Flashcards

1
Q

There are positions within genomes where large heterochromatin blocks are built called _______. Genes that are close to or within these areas are strongly repressed.

A

Silencers

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2
Q

The repression of genes by silencers depends on their ________, depending on whether they are close to or within heterochromatin. This does not depend their promoters.

A

Position

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3
Q

List two examples of positional repression from the model organism S. cerevisiae?

A
  1. Mating type loci
  2. Sub-telomeric genes
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4
Q

Describe main points surrounding the mating type loci in yeast, HML and HMR.

A
  • HML and HMR are constantly repressed.
  • Genetic studies have showed several proteins that regulate this repression.
  • Rap1 binds next to the repressed loci and recruits Sir proteins
  • Sir proteins (Silent Information Region) proteins spread over the repressed locus
  • Sir is a histone DEACETYLATES the histones at HML and HMR
  • The deacetylated histones bind tighter to DNA, form heterochromatin and prevent the association of transcriptional activators to the promotors
  • Histone hypo-acetylation is necessary for gene repression
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5
Q

Sir2 is a histone deacetyase. What does this mean?

A

It deacetylates the histones at HML and HMR.

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6
Q

Describe positional repression at the telomeres.

A
  • Rap1 and Sir proteins bind to the telomeres.
  • Sir proteins spread in the sub-telomeric regions of the chromosomes.
  • Many telomeres cluster at the periphery of the nucleus and are covered with condensed hypoacetylated nucleosomes
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7
Q

Describe the mutational analysis conducted on histones: Lysine –> Arginine

A
  • These mutants MAINTAIN gene repression at telomeres.
  • Arg retains the positive charge, can not be acetylated to lose its positive charge
  • The DNA-histone interaction is strong, chromatin is compact
  • Gene repression cannot be reversed by acetylating the histones
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8
Q

Describe the mutational analysis conducted on histones: Lysine –> Glutamine

A
  • These mutations ABOLISH repression at the telomeres
  • Glutamine has a neutral charge (resembling acetylated Lysine)
  • Glutamine cannot be deacetylated to gain a positive charge
  • Chromatin is decondesnsed
  • Gene cannot be repressed
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9
Q

Does the Lysine –> Glutamine mutation abolish or maintain gene repression at the telomeres?

A

Abolish -> Can not be deacetylated to gain a positive charge

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10
Q

Does the Lysine –> Arginine mutation abolish or maintain gene repression at the telomeres?

A

Maintains- Arginine retains the positive charge

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11
Q

In the case of positional repression, describe the role of Rap1, th telomere, Sir3/Sir 4, and Sir 2.

A

Rap1 - The repressor.
The telomere - The “Silencer”
Sir 3/Sir 4 - Co-repressors
Sir 2 - Histone-Deacetylase

The Sir2/3/4 complex binds Rap 1 and then spreads away from the telomere.

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12
Q

In the case of promoter-dependent repression and activation, ______ and ______ bind to promoters and enhancers and recruit the co-repressors or co-activators.

A

Repressors and activators (THESE DO NOT SPREAD)

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13
Q

In the case of promoter-dependent repression and activation, is the position of the gene a critical factor?

A

No.

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14
Q

Describe Ume6 and Sin3/Rpd3.

A

Ume6- Transcription repressor

Sin3/Rpd3 - Complex is a co-repressor

Rpd3- Histone deactylase

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15
Q

Transcriptional repressors often ______ interact with a histone deactylase.

A

Directly

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16
Q

Transcriptional repressors often ______ interact with a histone acetyl-transferase.

A

Indirectly

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17
Q

Describe Gcn4, SAGA and Gcn5.

A

Gcn4 - Transcription activator
SAGA - Complex co-activator
Gcnc5 - Histone acetyl-transferase

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18
Q

Ayceylated histones can recruit more co-activators via _______.

A

Bromo-domains

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19
Q

Transcriptional activators de-condense chromatin via 1. ________ and 2. ___________.

A
  1. Histone acetylation
  2. Chromatin remodelling
20
Q

What are the two types of co-activators brought in by transcriptional activators?

A
  1. Histon acetyl-transferases
  2. Chromatin-remodelling complexes
21
Q

All chromatin remodelling complexes are homologous to the yeast ________ complex

A

SWI/SNF

22
Q

Once histones are acetylated, nucleosomes- DNA interaction become _________.

A

Loose

23
Q

What do chromatin-remodelling complexes use to push nucleosomes along DNA to “open” promoters?

A

ATP (energy source)

24
Q

How do SWI/SNF ATPases function?

A

They move nucleosomes along the DNA by sliding or transferring them. They shift nucleosomes away from the promoter/enhancer sites and gives transcription factors access to the DNA.

25
Q

The mediator is an examples of a co-activator. The mediator is a huge complex containing a variety of proteins including enzymes and proteins that recognize ______, _______, and ______.

A

They recognize activators, GTFs, and other coactivators.

26
Q

True or False. Different mediators contain proteins required for all the same/every type of gene.

A

False - Different mediator complexes contain proteins required for specific genes.

27
Q

The Mediator directly interacts with ____________. One mediator complex can interact with multiple transcriptional activators.

A

Transcriptional activators.

28
Q

Cells differentiate and select the genes they ________.

A

Express

29
Q

Cells divide multiple times and express the ____ genes after each cell division.

A

Same

30
Q

True or False? DNA replication is a major disruptor of chromatin and bound transcription factors.

A

True.

31
Q

How do cells remember which genes to express?

A

The epigenetic memory of transcription. The “memory of gene expression is achieved through reconstitution of the same chromatin structure after the passage of the replication fork.

32
Q

How is epigenetic control of transcription maintained?

A

Through DNA methylation and methylation and acetylation of histones.

33
Q

When are epigenetic marks rebuilt?

A

Epigenetic marks are rebuilt during and/or soon after the passage of the replication fork.

34
Q

Name the three types of histone post-translational modifications?

A
  1. Methylation
  2. Acetylation
  3. Phosphorylation
35
Q

Methylation of CpG islands leads to ________.

A

Condensation of chromatin.

36
Q

How does methylation of the CpG islands lead to condensation of chromatin?

A
  • Methylated DNA recruits special classes of Me-DNA-biding proteins (MeBPs).
  • MeBPs recruit factors that deacetylates histones and condense chromatin.
37
Q

Unmethylated CpG islands recruit proteins that methylate a specific position on histones: ___________.

A

Histone 3-Lysine 4 (H3-K4). This is an epigenetic mark that dictates gene expression.

38
Q

The methylation of DNA is rebuilt _______ after the passage of replication forks.

A

Immediately

39
Q

Example: Methylation of the CpG islands in the promotors of tumour suppressor genes 1. ___________ their expression and 2. _______ cancer.

A
  1. Block
  2. Promote
40
Q

When the replication fork passes through the condensed chromatin, the cell _________ condensed chromatin.

A

Replicates or rebuilds

41
Q

When the fork passes through open chromatin, the fork rebuilds what kind of chromatin?

A

Open chromatin.

42
Q

What is the effect on transcription at the H3 (K4) site of modification with methylated lysine?

A

Activated transcription.

43
Q

What is the effect on transcription at the H3 (K9, K27) site of modification with methylated lysine?

A

Repression of transcription.

44
Q

Cells express the same genes after DNA replication and cell division through reconstitution of the same type of chromatin after the passage of the fork. How?

A
  1. Reconstitution of the H3-K9Me after the passage of the replication fork

(old histones with marks are recycled and assembled in the nucleosomes behind the replication form, while histone-methyl-transfereases recognize the H3-K9Me marks and methylate new histones re the site to build the same epigenetic mark)

  1. Reconstitution of H3-K27Me after the passage of the replication fork.

(Polycomb repression complex 2 is a H3-K27 methyl transferase that acts as a co-repressor and associates with heterochromatin, while the transcription repressors and PRC2 are recycled and rebuild behind the form the methylate H3-K27).

45
Q

Polycomb Repression Complex 2 (PRC2) maintains repression by associating with target loci and continually methylating ________.

A

H3-K27

46
Q

Polycomb Repression Complex 1 (PRC1) recognizes H3-K27-Me and _______ chromatin.

A

Compacts

47
Q

What is the role of trithorax function during chromosome replication?

A

It opposes repression by Polycomb complexes by METHYLATING H3 at lysine 4 and maintaining this activity during chromosome replication.

Therefore, methylating = activating transcription

MCB2050 Part 1 (13 decks)

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