How to identify transcription factors binding to an specific DNA sequence? - (Aug/23/2007 )

Hi, ALL,

My boss have an idea to identify the transcription factors binding to a specific DNA region. We don't have any transcription factor candidate, only what we have is a potential promoter region of an gene. Does anyone have any idea what I should do, what techniques should I use?

Thank you very much.

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Under the conditions you think that the transcription factor binds, you can cross-link the transcription factor to the promoter, isolate the DNA/protein complex then study the protein e.g. by immunoprecipitation. Check out this article for a start.

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to predict TFBS, the most used software is TRANSFAC, but this requires a subscription. Earlier versions of the software are freely available, you can find some of them on this web site (http://www.gene-regulation.com/pub/programs.html) You can find free alternatives on the web, just google for transcription factor prediction.

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Well, if you don't have any candidate TF you can always go for an yeast one-hybrid assay. You can analyse a whole transcriptome (statistically) with this approach. The catch is that you need a cDNA expression library for the screen...

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Thanks all of you very much. I know nothing about the technique what I need, I will read some background according to what you guy recommend. I might ask more question. Thank you again.

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Hi Daniel,

I found your posted in Bioforum. I am using the CloneTech Match maker Screeing Kit (yeast one hybrid) to screen the transcription factor binding with the promoter of gene. I did not have any problem with the yeast growing, my colonies look very healthy, but I can not find any potential transcription factor. If you are working with transcription factor screening, I will be very appreciated, if you can share the idea in the experiment with me.

Nitima Suttipanta

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