Transcriptional Regulation - Eukaryotes

Question 1

How can eukaryotes regulate transcription?

Answer 1

Using repressors and activators and also chromatin remodelling

Question 2

Where is the regulatory region of a eukaryotic gene?

Answer 2

Before the core promotor - where the transcription factors bind

Question 3

What binds in the regulatory region of a gene?

Answer 3

Repressors and activators

Question 4

What are 2 ways a transcriptional activator can increase transcription in eukaryotes?

Answer 4

Either directly by recruiting RNA polymerase or indirectly by recruiting general transcription factors

Question 5

Is it general or specific transcription factors that are responsible for gene regulation?

Answer 5

Specific

Question 6

What are regulatory sequences that are very far from the promotor called?

Answer 6

Enhancers

Question 7

How are enhancers brought closer to the promotor that it is regulating?

Answer 7

Looping of the DNA

Question 8

What binds to enhancers?

Answer 8

Specific transcription factors that increase transcription

Question 9

What are insulators?

Answer 9

DNA sequences bound by proteins that block the function of enhancers

Question 10

Say an enhancer is between two genes and is the same distance from both. What makes it regulate the gene it is supposed to regulate and not the other one?

Answer 10

An insulator will be between the enhancer and the gene it is not supposed to regulate. It will block the enhancer from looping to that gene, so it defines which genes are acted on by that enhancer

Question 11

Does looser or tighter chromatin favour increased transcription?

Answer 11

Looser

Question 12

Does tighter chromatin mean it is heterochromatin?

Answer 12

No, it is still referring to euchromatin that is slightly tighter or slightly looser. Transcription only happens in euchromatin

Question 13

What are 3 general ways chromatin is loosened or tightened?

Answer 13

1. Slide nucleosomes along the DNA
2. Remove a nucleosome
3. Squish nucleosomes together

Question 14

What was the experiment that showed how chromatin remodelling can change gene expression over the course of development?

Answer 14

They used DNase I, which can’t any DNA that is bound to histones or that is more tightly packaged. Examined how susceptibility to DNase I changed over the development of a chick embryo in one embryonic globin gene and two adult globin genes. None of the genes got cut after 24 hours, only the embryonic gene got cut after 5 days, and only the adult genes got cut after 14 days. It didn’t get cut in cells where it wasn’t supposed to be expressed either

Question 15

What is the chromatin remodelling complex?

Answer 15

Proteins that can reposition nucleosomes

Question 16

What recruits the chromatin remodelling complex?

Answer 16

Transcriptional activators and repressors

Question 17

What are histone tails?

Answer 17

Parts of the histone proteins that extend out of the nucleosome for higher levels of packaging

Question 18

What are the 4 covalent modifications that can be made to histone tails to promote chromatin remodelling?

Answer 18

Acetylation, methylation, phosphorylation and ubiquination

Question 19

What enzymes add acetyl groups to histone tails? Which enzymes remove them?

Answer 19

Acetyltransferases add them, deacetylases remove them

Question 20

Does acetylation tend to promote more loosely or more tightly packed chromatin?

Answer 20

Looser

Question 21

What enzymes add methyl groups to histone tails? Which enzymes remove them?

Answer 21

Added by methyltransferases, removed by demethylases

Question 22

How do the histone tail modifications have meaning to other proteins?

Answer 22

They are read like a code and tell the chromatin remodelling complex whether to loosen or tighten the chromatin

Question 23

Does methylation tend to promote more loosely or more tightly packed chromatin?

Answer 23

Depends on which amino acid it is attached to

Question 24

How can DNA be modified to cause chromatin remodelling?

Answer 24

Methylation of cytosine bases

Question 25

Does DNA methylation increase or repress transcription?

Answer 25

Represses it. Methylated DNA is more tightly packed

Question 26

How does methylated DNA cause chromatin to become tighter?

Answer 26

It recruits histone tail deacetylases

Question 27

What is the advantage of methylating DNA over methylating histone tails?

Answer 27

Stronger bond in DNA, which makes the repressed state stick around longer

Question 28

What are the 3 mechanisms that cause chromatin remodelling?

Answer 28

1. Direct recruitment of the chromatin remodelling complex
2. Indirect recruitment through histone modification
3. Indirect recruitment through DNA methylation

Question 29

How does direct recruitment of the chromatin remodelling complex work?

Answer 29

An activator or repressor binds to a regulatory sequence. That recruits the chromatin remodelling complex and loosens or tightens the chromatin

Question 30

How does indirect direct recruitment of the chromatin remodelling complex through histone modification work?

Answer 30

An activator or repressor binds to a regulatory sequence. That recruits a histone modifying enzyme which adds or removes modifications on the histone tails. The modifications recruit the chromatin remodelling complex and the chromatin becomes looser or tighter

Question 31

How does indirect recruitment of the chromatin remodelling complex through DNA methylation work?

Answer 31

An activator or repressor binds to a regulatory sequence. That recruits DNA methyltransferase that methylates the DNA. The methylated DNA recruits a histone modifying enzyme that removes histone modifications. That recruits the chromatin remodelling complex which tightens the chromatin

Question 32

How does coordinated regulation of gene networks occur in eukaryotes?

Answer 32

At the level of the transcription factors. They can be regulated by the same specific transcription factors

Question 33

Do eukaryotes have operons?

Answer 33

No