Experimental method to count the mean number of DNA-bound transcription factors

Question

[Pascal]

Hello everyone,

I was wondering if there is an experimental method to count the number of bound transcription factors on a promoter?

So, for example, you have a promoter/enhancer region with 5 transcription factor binding sites (TFBS), and you know that not all TFBS need to occupied to initiate transcription. How would one determine the mean number of occupied binding sites? And how for a promoter that has 2 TFBS, or for one that has 10 TFBS?

Thanks for your help,

Pascal

[Amitm]

I don't know the answer but its interesting! How to determine how many sites are occupied rather than looking for all possible sites of a particular TF (through ChIP-Seq)?

Maybe DNAaseI sensitivity data? Though I am not sure it would be able to resolve 'closely' spaced TFBS'

[Pascal]

How closely spaced is 'closely spaced' in your opinion?

[Amitm]

I am not sure. I have not worked with DNase/ open-chromatin (high-throughput) datasets and hence my understanding is limited to that gained from looking into related reviews now & then.

But what I meant was suppose upstream of gene X there are 3 TFBS, all within a 300bp stretch. And the DNaseI data says there is a sensitive/ open chromatic region of 550bp (encompassing completely the 300bp above). Then it would not be feasible to tell if all 3 TFs were bound or a combination. Again, I have not looked into the data so I am hand waiving. Maybe you could look for a couple of genes and test if you are able to make sense