Hi jibin,

If you know the regulatory sequences upstream of the target proteins, you can clone then in reporter vectors and use your protein to activate these vectors in, for instance, a luciferase assay.

Another option is to pulldown the protein and then, first, check whether it is pulling down DNA and additionally you can amplify the DNA with random primers and send the product to sequence for identification of regulatory sequences.

There are also Chip-based method/kits but I never used then before. Surely you'll get more updated state-of-the-art solutions from the RG community.

Cheers!

Hi Sebastián,

Thank you very much. I'd like to try the second option you suggested at first, because I am planning to do ChIP-Seq for another project.

Cheers!

Hi Lucia,

Thank you for the enlightening suggestion. There are several DNA binding domains (Edgar Wingender 2013, 2014). What I can think of is to align the interest sequence with the TF DNA binding domain one by one. Is any better tools available, please?

Thank you again,

Jibin

an indirect way would be to check where it binds by chip-qpcr...some people suggested emsa but i am more in favour of doing chip-seq you can find a motif (if any) afterwards bioinformatically....even more old-fashioned you can do Selex...

get rid of it by shrna or cripr if you want and see if it has any effect

purify it and do more specific transcription assays though am not sure how easy these are to interpret

anca

Grande Anca!!!