Question about eukaryotic promotors - (Sep/17/2005 )

Hiho,

i have a question regarding promotors /enhancers in general.....im still studying and i was not able to get this problem solved by consulting several books, so i decided to ask you guys here, because i saw a concentration of knowledge in this forum

if we look at an eukaryotic promotor we got first the typical core-promotor (BRE, TATA, Inr, DPE)depending to our gene.....thats fine.
in addition to that we can have a set of general available upstream elements like the GC-box or the CAAT-box and Octamer e.g. to regulate the frequency of our transscription.

to regulate our expression due to different signals there are certain response elements like the GRE, SRE, HRE with their specific TF's etcetera.

ok, thats what i know....but my question is....we got shitloads of transscription factors in our cell, every one of them has to be able to bind to a certain sequence in order to have an activating or suppressing influence to his target-gene.

Are there TF's with their very "own" binding-sequence/response-element depending on the aminoacids they are using to make contact to the major groove....? or are they recognizing only different sets of standard-sequences with different consensus-sequences?

if someone know the answer to this question i would really appreciating it, because this question is killing me
dont get me wrong, i dont want you to answer exam-questions for me, but this is just a thing i dont really get by reading in my books.


edit: i got my answer....... sometimes writing about a problem helps remembering how things work^^

for example the recognition of GRE's by different steroidreceptors containing zinc-finger domains, which can bear various aminoacids for binding.....the response element consists of half-sites and the distance between these halfsites and their sequence determine the specifity for the binding homodimers...correct me if im wrong
i guess its similar to other TF binding sites ...specifity comes by varying consensus-sequences and maybe the distance between them for binding by dimers.

anyway, im tormenting my brain now with another question......does someone know how to prove that e.g. polymerase binds to dna?

i guess it would be done with an emsa followed with an footprinting, wouldnt it?

edit: uh...sorry....i totally overlooked the "basic biology questions" forum down there....could maybe a mod move it to there?