Flashcards in Regulation of Gene Expression Deck (21):
___ bonds are important in DNA/protein interactions
(Arg is +)
what are transcription factor structural domains
1. zinc finger: steroid hormone receptors (ER, PR, AR, GCR)
2. helix - turn-helix: homeodomain proteins; impt dev and are responsible for making specific structures. Modify Hox genes.
3. Leucine Zippers: (hydrophobic) involved in protein/protein interactions. (AP-1) Bind to enhancer elements and recruit RNA pol and accesory proteins to core promoter.
4. activation domains: interact with RNA pol. They're highly acidic or glutamine -rich regions.
Whats electrophoretic mobility shift assay?
Looks for TF activation and whether/ not a specific TF is in nucleus. Take DNA and radio label it. Consensus seq of 20 bp. Center is binding site for NFkB. Take proteins from cells and isolate the nuclei, and nuclear proteins and throw them with radio labeled DNA. DNA/protein is then loaded onto a non-denaturing polyacrylamide gel.....if NFkB in nucleus bc its been act by something it will bind to consensus seq and shift mobility of the radio labeled piece of DNA. It will be heavier and migrates more slowly Cells were exposed to LPS which stimulates NFkB to go to nucleus. If non specific protein it bind to non specific seq.
Which enzymes are used in transcription activation?
1. TF bind to enhancers and recruit modification and remodeling enzymes. It recruits chromatin modifier proteins, aceytlates histones and demethlate DNA.
2. HMG proteins
3. Mediator makes complex come together and interact with RNA pol
4. TATA box at -30 upstream of Trans start site.
How is transcription repressed?
1. Block recruitment of chromatin modifying machinery or recruit machinery that methylates DNA to silence it.
2. Block interaction bet enhacers and mediators
-Glucorticoids did this for NFkB.
What is the stepwise process of transcription activation
Activators, TF go first, recruit chromatin modifiers, TF bind to DS DNA in enhancer regions. Coactivators help complex come together and respond to each other. RNA pol II sits at core promoter in Inr region to start transcription. Begins with TATA box binding protein, binding to TATA box. Once DNA is rearranged, RNA pol II sits there until TF 2H phosphoryaltes carboxy terminal domain which then gets released to start transcription.
Many TF have both DNA binding domains and ____ domains. Transactivation domains are proline rich ___ rich or acidic
What are micro-RNAs ?(small interfering RNAs)
mediate the silencing of many genes and can be involved in the formation of heterochromatin. Some interact with mRNA usually in 3' UTR and cause mRNA degradation or causes inhibition of translation.
_____ is an enzyme that cleaves ds RNA which become ss and pair with mRNA which then gets degraded or not translated
we find stRNA (small temporal) in ____ and siRNA (small interfering) in research lab
How do some proteins mediate translational repression.
Some phosphorylate eIF3 or eIF4E and block eiF4g to block iniation to transcript which doesnt get translated.
What are stages of tooth dev?
1. dental lamina: epthelial band where teeth form
Barx and MXS: TF req for specific structures.
Gly responds to SHH
2. Bud stage:
3. CAP stage
4. Bell stage
What gene is required for tooth development in mouse embryo?
____Inc exp of Pax 9. ____ and ____ decrease exp of Pax 9
FGF8; BMP2 &4
What's important in tooth dev?
growth factors from epithelium dictate which TF are active in underlying mesenchyme or whether/ not tooth dev in that specfic region.
what are the stages of mouse tooth dev
1. initiation: oral epi induces formation of the dental lamina
2. bud stage; epi tooth bud forms; surr mesenchyme condenses
3. cap stage; dental papillae and enamel knot form. the cells of the enamel know will direct final tooth structure before dying via apoptosis
what type of signaling is in each stage of mouse tooth dev?
1. initiation: epithelial signaling
2. bud: mesenchymal
3. cap: enamel knot
molar vs incisor is det by growth factor signaling from overlying ____ (FGF-8 vs BMP-4) and homeodomain proteins (TF) in mesial and distal mesenchyme: ____ vs ____
epithelium; MSx-1 and Barx-1
What did the incisor vs molar signaling experiment show us? how did it work?
took out tooth buds and packed with beads called proteins called Noggin which is a BMP-4 inhibitor so no longer inhibition of Barx-1 or activation of MSx-1 so the influence of Barx-1 encroaches into the main yellow region. Took packed tooth bud and put it in renal capsule which is very vascular and provides tissue with all the nutrients it needs to grow and left it there for a while and took it out and looked at what tissue had grown in renal capsule sample. incisor + noggin looked like molar by blocking 1 TF and allow a diff TF to encroach on that region which shows us that changing/directing the specfics of a tissue by TF is possible.
FGF-8 inc ____which induces molars. BMP-4 inhibits Barx-1 and activates ____which gives us molars.