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14 Cards in this Set

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What is a two hybrid experiment?


What would be the best technique to ID a specific DNA sequence to which a protein binds?

ChIP-Seq Assay


Zinc finger domain vs zinc cluster domain

Finger has three domains that interact with the DNA

Leucine Zipper

Coiled coil region, helices insert into the major groove. They often form heterodimers.

Activation domains

often made up of small units of repeated acidic and hydrophobic amino acids. they usually bind to the mediator complex or the TFIID.

Activators brings in nucleator modifiers: examples

chromatin remodeling complex and histone acetyl transferase

What is the purpose of nucleosome anchors?

They position the nucleosome and facilitate activator binding.

What is NELF complex?

It induces stalling shortly after initiation. The stalling allows for activators to recruit SEC( Super elongation complex).

What is an example of an activator that recruits elongation factors?

Drosophila HSP70 heat shock, causes formation of HSF which replaces H2B allowing Pol II to leave. It also recruits P-TEFb which phosphorylates;

Mixed lineage leukemia

Is related to the stalling problem. you need more detail on this guy. Basically what happens is there is a fusion between protein complexes. The most common is theAFF1

Purpose of insulators
If there is an insulator betweenthe enhancer and the promoter, expression from that promoter will be turnedoff. They also insulators are a way ofcontrolling which promoter is activated by a distant enhancer.
Locus control region
LCRs contain multiple elements –enhancers, insulators and even promoter-like sequences. LCR work in conjunction withother activators for each gene to determine which is expressed when duringdevelopment.
What are the ways activators interact?
Cooperative bindingof activators:Four ways that the binding ofone protein to a site on DNA can help thebinding of another to a nearby site. (a)Cooperative binding through direct interac-tion between the two proteins is shown. (b) A similar effect is achievedby both proteins interacting with a commonthird protein. (c,d) Indirect effects in whichbinding of one protein to its site on DNAwithin nucleosomes helps binding of asecond protein. (c) The first protein recruitsa nucleosome remodeler whose actionreveals a binding site for a second protein.(d) The binding of the first protein to its siteon the DNA just where it exits the nucleo-some. By binding there, it unwinds theDNA from the nucleosome a little, revealingthe binding site for the second protein.Each of these mechanisms can explain howone regulator can help others bind or,indeed, how an activator can help the tran-scriptional machinery bind to a promoter.
How does activation of HO endonuclease work?
It requires the work of two activators. SWI5 and SBF. SWI5 recruits chromatin remodeling complex (SNF) and histone complex. SBF activates the HO gene.