how to find the transcrition factor binding sites! i'm a beginner - (Nov/07/2007 )

i have verified a certain transcription factor binds the promotor using ChIP, but how to get the exact location within the promotor and the sequence of the binding site?
is it necessary to know before studying exactly how the transcription factor regulate the transcription process?


thanks!

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We verify our promoter for probable transcription factor binding sites by genomatix first. Then do CHIP for the particular site if it is positive we go for promoter analysis by cloning that piece of promoter and reverifieng for luciferase activity.
Hope this helps.....

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thank you for your reply!
by the way,is it necessary to sequence the ChIP product? or just run it on gel to see the band?

and i have some problem that i can't figure out the reason, after the ChIP i just resuspended the DNA in 24 μl TE buffer and PCR an aliquot of 8μl and run it on 1.5% gel and got the band, i saved the other two tube at -20. but the next day i failed to see the band using the other two tube,i was confused, why? is it degraded? i need help

any suggestion would be greatly appreciated

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We just run the CHIP product on the gel.
Quite interesting DNA resuspended in TE buffer should be stable. Some one else should answer this.

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