evaluation of tf binding motifs

Cattaruzza at veg-physiol.med.uni-goettingen.de Cattaruzza at veg-physiol.med.uni-goettingen.de
Thu Sep 24 12:07:27 EST 1998

dear collegues,
currently we are trying to analyse a 5´-noncoding sequence of about 1200
bp. this sequence occurs to have a negative regulation site.
bright like we are, we decided to screen the sequence for putative binding
sites of dna binding proteins (we are physiologists....).
when i did this using internet resources like transfac... i got, depending
of the (in my understanding arbitrary) threshhold between 30 and 100
binding motifs: shocking.
lots of them should not be interesting in our goi (sex related motifs like
sry, sox and so on) other motifs like gata occur very often but who should
wonder about this?
so, i got virtually no information from this search.
then i tried to find out if at least those promotorsequences have more of
such binding sites than coding sequences: you might guess the
result....there are some coding sequences with fewer but also lots of them
with very high amounts of "binding motifs" ( which might not be too
surprising when one thinks about  4-10 nucleotide motifs in long sequences).
 so, finally, my question to all people who are professionals in this
strange field of research (sorry):

what is the significance of a given binding site? and, if per se, there is
no significance (ap-1, nfkappab, cebp and all the other factors will not
"glue" all the coding sequences in the genome, will they? are there enough
of them?) what makes a binding motif "sticky" for a factor? when is it
regulatory? how can one find out? if it is space/distance in regard to
other factor binding sites (with bound factors) is there a program out
there which might predict active "binding motif clusters"?

thank you in advance, i would really appreciate any hints for literature,
software or good thoughts about that topic.

p.s.: apart from that: might our negative regulatory element (and most in
the literature for mammalian sequences) be due to too big vector
constructs, which are simply better expressed, when there is cut out let´s
say 1200 bps? a unconfortable idea....

Universitaet Goettingen
Zentrum Physiologie und Pathophysiologie
Abteilung Vegetative Physiologie
Marco Cattaruzza                  Tel 0551-395891
Humboldtallee 23                  Fax 0551-395895
37073 Goettingen                  Mail:catta at veg-physiol.med.uni-goettingen.de

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