Dear Stojkova,

I had experience to do ChIP-PCR before, but I used eukaryotic cells. As I know, if your protein has no spesific binding in dsDNA, you won't get the positive result in PCR/Western blot. I am sorry if my answer didn't help you.

I would like to use ChIP-seq, but despite thank you for your contribution.

Every transcription factor recognizes a DNA binding motif. Try to look for its homologous protein in literature and see if you can come across any established DNA motif. That might give you a lead while looking for sequences upstream of promoter regions/RNA polymerase binding site. Use 500 bp upstream sequence as a search query to find RNAP binding site using online programs like http://bip.weizmann.ac.il/toolbox/seq_analysis/promoters.html#prokaryote. Once you have found it you can search for additional sites if you know what genes it controls. Keep in mind that in CHIP-Seq, you will get some non-specific reads but that will fall within noise level as long as you get good signal for specific DNA motif. You should also be able to test few (if possible known) sequences containing DNA binding motif using DNAse digestions to verify your ChIP-Seq results.

You can refer to my paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681086/

Hope this helps!