Lesson 15: Eukaryotic Gene Regulation

Question 1

What is an enhancer?

Answer 1

Where transcription regulators (ex: activators, repressors) bind to enhance transcription

Question 2

Can enhancers be far away from the promoter?

Answer 2

YES!

Question 3

What does an activator do in an eukaryotic cell?

Answer 3

• It promotes the formation of the transcription initiation complex (general transcription factors, mediator, and RNA polymerase II)
• It increases the transcription initiation complex’s ability to bind to the promoter
  NOTE: The activator has two binding spots one that binds to the mediator and the other binds with the enhancer

Question 4

What does a repressor do in an eukaryotic cell?

Answer 4

• Physically block activators or general transcription factors/RNA polymerase II by binding DNA
• Bind activators to prevent the activator from binding to the enhancer

Question 5

How do we turn on many genes at once to respond to the environment or during development?

Answer 5

a SINGLE transcription factor can activate many genes required to respond to the environment and/or during development.
- NOTE: The coding sequence can be on either strand of DNA
- NOTE: Also, this is similar to the operon, HOWEVER, these genes can be anywhere in the genome, they do not have to be near each other (not be made in a single mRNA). Since eukaryotic mRNA is monocistronic, you cannot have multiple genes on one strand. Instead we can put the same enhancer in front of several genes and the enhancer will be recognized by the same transcription factor allowing for it to activate many genes at the same time.

Question 6

Can a combination of transcription regulators be used to turn on gene expression?

Answer 6

YES!
- Many times cells will express various combinations of transcription regulators will work together to drive expression of genes required for that cell’s function

Question 7

How can a limited number of transcription regulators generate many different cell types?

Answer 7

Different combinations of these transcription regulators can be used

Question 8

What is a master regulator?

Answer 8

Expression of a master regulator can create an entire organ. Master regulators drive the expression of many genes. Those genes (and the genes they control) dramatically alter the cell’s fate and function. -> KIf4 is an example
ex: eye structure on the leg

Question 9

How do these master regulators work in a positive feedback loop?

Answer 9

These master regulators can bind their own promoters (therefore drive their own expression) and bind to other regulatory regions (so drive other master regulators’ expression)

Question 10

How is combinatorial control of gene expression shown in eukaryotes?

Answer 10

1) Several transcription regulators can work together to determine the expression of a single gene
2) Combinations of transcription regulators can drive gene expression to control cell fate

Question 11

What are stem cells?

Answer 11

• unspecialized
• potent (have the ability to become another cell type)
• able to divide and make another stem cell (self-renewed)

Question 12

What are the types of stem cells?

Answer 12

1) Embryonic
2) Adult
3) Induced Pluripotent Stem Cells (iPSC)

Question 13

What is Waddington’s Landscape?

Answer 13

The idea that as development occurs (as a cell “falls” down the hill), potency decreases.

• Different cell fates are driven by the changes in gene expression.

CONCLUSION: the final state is stable such that the ball can’t roll back up the hill

Question 14

What is unipotent?

Answer 14

Lowest potency, most specialized
ex: differentiated cell types

Question 15

What is multipotent?

Answer 15

Some cell types, but limited
ex: adult stem cells

Question 16

What is pluripotent?

Answer 16

Most cell types but not all
ex: iPSC, embryonic stem (ES) cells, EG cells

Question 17

What is totipotent?

Answer 17

Highest potency
ex: zygote

Question 18

Can we roll back up the hill?

Answer 18

YES!

Remember -> Sir John Gurdon showed that putting the nucleus from a differentiated frog cell into an egg cell with the nucleus removed could become a whole organism. Shows that cells could g from being an adult to back to a tadpole.

Also, in 2006/2007, Dr. Shinya Yamanaka isolated skin cells and pushed them back in developmental time to an embryonic-like cell state/ These cells are called induced pluripotent stem cells (iPSCs)

Question 19

How were these adult cells reprogrammed into embryonic-like stem cells?

Answer 19

Expression of three transcription regulators (master regulators -> Oct4, Sox2, KIf4)
- These transcription regulators were introduced to the adult cell then allowed to divide. Then cells began to differentiate

Question 20

What does epigenetics mean?

Answer 20

“above” the genetic code

• Involves modifications to DNA-associated proteins and DNA itself that alters how the DNA is “read” rather than alteration of the genetic code itself

Question 21

What are more characteristics on epigenetics?

Answer 21

• Epigenetic changes occur during development and in response to the environment
• As cells become specialized they have their own unique epigenetic profile
• Changes in the epigenome can be inherited upon cell division
• Reversibility allows organisms to respond to their environment

Question 22

What are the different types of epigenetic modifications?

Answer 22

1) Histone Acetylation (and Methylation)
2) Chromatin remodeling factors
3) DNA Methylation

Question 23

How does the chromatin-remodeling complex and the histone-modifying enzyme regulate transcription?

Answer 23

When the chromatin-remodeling complex and the histone-modifying enzyme are brought to the promoter region. They drive whether or not DNA is accessible.

Question 24

How does DNA accessibility control what genes are expressed?

Answer 24

If the DNA is accessible, transcription regulators will be able to act, thus being able to express/repress the gene

Question 25

What does heterochromatin mean?

Answer 25

DNA is condensed and inaccessible to transcription machinery. Genes in the regions are OFF; may be referred to a “silenced” region of the chromosome

Question 26

What does euchromatin mean?

Answer 26

DNA is decondensed and open; genes in the region can be ON (cells also need appropriate transcription regulators expressed)

Question 27

How does the modification of histone tails affect histone’s interaction with DNA and other proteins?

Answer 27

• Acetylation occurs on Lysines
• Methylation occurs on Lysines or Arginines.
• Histone acetylation makes the DNA more open (euchromatin) because the acetyl groups neutralize the charge of histones
• Combinations of methylation and acetylation can be “read” by the cell to determine if the region should be open or closed

Question 28

How does histone acetylation promote transcription?

Answer 28

1) Addition of an acetyl group to histone tails by HATS (histone acetyltransferase) neutralizes the charge, loosening the histones hold on DNA, which IMPROVES access for DNA regulator proteins
2) Acetylated histones can also bind other proteins like chromatin remodeling factors to promote transcription.
3) Alters accessibility to promoter elements like the TATA box
- NOTE: Deacetylation by HDACs (histone deacetylase) has the opposite effect (tightens the histones hold on DNA which decreases transcription)

Question 29

How does chromatin remodelling complex promote transcription?

Answer 29

The chromatin remodeling complexes use energy from ATP hydrolysis to loosen the DNA and push it along the histone octamer
- NOTE: This complex can also make DNA less accessible (it can also decrease transcription)

Question 30

Where does DNA methylation occur?

Answer 30

It occurs on certain cytosine bases (usually found in CG pairs)

Question 31

How does DNA methylation decrease transcription (gene expression)?

Answer 31

DNA methylation tens to turn OFF genes in the area by recruiting in proteins that block transcription.