Lesson 15: Eukaryotic Gene Regulation Flashcards
What is an enhancer?
Where transcription regulators (ex: activators, repressors) bind to enhance transcription
Can enhancers be far away from the promoter?
YES!
What does an activator do in an eukaryotic cell?
- 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
What does a repressor do in an eukaryotic cell?
- Physically block activators or general transcription factors/RNA polymerase II by binding DNA
- Bind activators to prevent the activator from binding to the enhancer
How do we turn on many genes at once to respond to the environment or during development?
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.
Can a combination of transcription regulators be used to turn on gene expression?
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
How can a limited number of transcription regulators generate many different cell types?
Different combinations of these transcription regulators can be used
What is a master regulator?
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
How do these master regulators work in a positive feedback loop?
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)
How is combinatorial control of gene expression shown in eukaryotes?
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
What are stem cells?
- unspecialized
- potent (have the ability to become another cell type)
- able to divide and make another stem cell (self-renewed)
What are the types of stem cells?
1) Embryonic
2) Adult
3) Induced Pluripotent Stem Cells (iPSC)
What is Waddington’s Landscape?
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
What is unipotent?
Lowest potency, most specialized
ex: differentiated cell types
What is multipotent?
Some cell types, but limited
ex: adult stem cells
What is pluripotent?
Most cell types but not all
ex: iPSC, embryonic stem (ES) cells, EG cells
What is totipotent?
Highest potency
ex: zygote
Can we roll back up the hill?
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)
How were these adult cells reprogrammed into embryonic-like stem cells?
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
What does epigenetics mean?
“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
What are more characteristics on epigenetics?
- 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
What are the different types of epigenetic modifications?
1) Histone Acetylation (and Methylation)
2) Chromatin remodeling factors
3) DNA Methylation
How does the chromatin-remodeling complex and the histone-modifying enzyme regulate transcription?
When the chromatin-remodeling complex and the histone-modifying enzyme are brought to the promoter region. They drive whether or not DNA is accessible.
How does DNA accessibility control what genes are expressed?
If the DNA is accessible, transcription regulators will be able to act, thus being able to express/repress the gene
What does heterochromatin mean?
DNA is condensed and inaccessible to transcription machinery. Genes in the regions are OFF; may be referred to a “silenced” region of the chromosome
What does euchromatin mean?
DNA is decondensed and open; genes in the region can be ON (cells also need appropriate transcription regulators expressed)
How does the modification of histone tails affect histone’s interaction with DNA and other proteins?
- 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
How does histone acetylation promote transcription?
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)
How does chromatin remodelling complex promote transcription?
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)
Where does DNA methylation occur?
It occurs on certain cytosine bases (usually found in CG pairs)
How does DNA methylation decrease transcription (gene expression)?
DNA methylation tens to turn OFF genes in the area by recruiting in proteins that block transcription.
