Regulation of Gene Expression

Question 1

DNA methylation:

• What is the role of cpG islands?
• hyper/hypomethylation does what?
• DNMT enzymes do what?

Answer 1

• Methylation of DNA occurs on cytosine residues adjacent to guanines (CpG dinucleotides) by DNA methyltransferase (DNMT) enzymes.
• clusters of regulatory CpG dinucleotides within promoter regions are referred to as CpG islands.
• The promoters of active genes are sparsely methylated, whereas silenced genes are associated with hypermethylation.

Question 2

Is vimentin expressed in fibroblasts and epithelial cells? Why/why not?

Answer 2

Vimentin highly expressed in fibroblasts, but not in epithelial cells due to methylation

Question 3

Disorders with methyl binding protein MeCP2

Answer 3

autism and Rett syndrome

Question 4

HATs do?

Answer 4

Histone Acetyl Transferases (HATs) add acetyl groups onto histone tails.

Question 5

Where are acetyl groups added? What charge does this area usually have? What effect does this have on affinities for DNA? Overall more or less transcription?

Answer 5

Acetyl groups are added to lysine residues on the histone tails that normally have a positive charge.
Adding the acetyl group reduces the attraction of the histone tail for DNA, resulting in in a more open configuration of the chromatin and easier access for transcription factors to bind to the DNA. MORE TRANSCRIPTION

Question 6

How does acetylation help the transcription factor TFIID?

Answer 6

TFIID has two bromodomains that bind onto acetyl groups

Question 7

Does methylate activate or silence DNA?
How can it affect acetylation?
What else might histone methylation do? Think transcription process…

Answer 7

• can be associated with gene activation or gene silencing
• Methylation of certain residues may block acetylation
• Histone methylation also plays a role in transcriptional elongation

Question 8

What does acetylation do for H3K9? What about methylation?

Answer 8

acetylation with H3K9ac opens transcription. If methylated, HP1 is recruited, which causes further methylation down the line.

Question 9

What do boundary elements do?

Answer 9

control spreading of heterochromatin, can silence things.

Question 10

What do nucleosome remodeling engines do?

Answer 10

Nucleosome remodeling engines can shift the position of nucleosomes allowing access of transcription factors to gene promoter regions

Question 11

Important note on promoters:

Answer 11

all promoters are different. They may contain some common elements, but they will be in a unique combination allowing for specific control of how efficiently an individual gene is transcribed at any particular time.

Question 12

What 3 basic things do activators do?

Answer 12

Bind DNA
Interact with GTF
Recruit coactivators

Question 13

basics of repressors

Answer 13

Bind DNA
Disrupt action of activators or GTFs
Recruit corepressors

Question 14

definition of enhancers

• location
• cooperation

Answer 14

a DNA sequence associated with transcriptional activation that is position and orientation independent. Can be far away, upstream or downstream. show synergy

Question 15

coactivators?

-3 ways they can help

Answer 15

proteins that do not bind DNA directly, but can bind to other proteins that are bound to the DNA.
• Bridging between gene specific activators and GTFs
• Scaffold for the formation of transcriptional complexes
• Histone acetylation (HAT) activity

Question 16

Passive repression? 3 ways?

Answer 16

“Passive” repression occurs when a repressor interferes with the function of an activator. This can occur by

1. preventing the activator from binding to the DNA
2. by binding to the activation domain
3. by preventing the activator from binding to the general transcriptional machinery.

Question 17

co-repressors with HDACs?

Answer 17

corepressors can recruit these histone deacetylating transferases, which remove acetyl groups.

Question 18

Translational control: Ferretin, Transferrin, and transferrin receptor

Answer 18

ferretin binds excess iron, and for storage in cells
transferrin is an iron transport protein in the blood
transferrin receptor binds transferrin and imports iron into cell

Question 19

In iron starvation, what will happen with ferretin and transferrin receptor?

Answer 19

decrease in ferretin, and increase in transferrin receptor

Question 20

In iron excess, what will happen to ferretin and transferrin receptor?

Answer 20

increase in ferretin, and decrease in transferrin receptor

Question 21

When is the siRNA pathway used? What do they do?

Answer 21

The siRNA pathway is used as a defense against viral infection. Endogenous siRNAs silence transposons and maintain heterochromatin.

Question 22

What processes and what are both siRNA and miRNA loaded in to?

Answer 22

Dicer processes both, and both loaded into RISC

Question 23

Perfect binding to mRNA target, results in mRNA cleavage explains which one? siRNA or microRNA?

Answer 23

siRNA

Question 24

Imperfectly binds to mRNA target and results in translational repression/mRNA degredation? siRNA or microRNA?

Answer 24

microRNA

Question 25

siRNA and microRNA are generally what? what purpose?

Answer 25

non-coding RNA that negatively regulate gene expression

Question 26

If iron is low, what does IRE-BP do?

Answer 26

Binds to IRE sequence on 5’UTR of ferretin mRNA, BLOCKING RIBOSOME from scanning, decreasing ferretin levels. IRE-BP binds to IRE sequence located on 3’UTR of transferrin receptor and acts as a shield from endonuclease activity. So, you get more transferrin receptor. Iron low= LESS FERRETIN AND MORE TRANSFERRIN RECEPTOR

Question 27

do coactivators bind transcription factors or DNA?

Answer 27

Transcription factors, NOT DNA.

Question 28

methylation in the open reading frame could still be an activated gene when/

Answer 28

If the promoter is acetylated.

Question 29

methylation of H3K4 does what?

Answer 29

enhances transcription