Promoter, Chip, transcription factors etc. - (Jul/21/2009 )
Hi everybody! I have a mouse strain lacking a gene. In tissues lysate derived from this mouse, there is a protein with increased expression compared to the wild type. When I add a chemical that compensate for the lack of the gene, the expression of the protein is downregulated. I am eager to know which transcription factor regulates an expression of the protein, but don't know how to do it. If I would wanted to check whether a given transcription factor binds to some promoter(s), I'd do Chip employing antibody against transription factor followed by PCR, but what to do in such sort of reversed situation? Many-many thanks for ideas! (I'll mention your help if get published in Nature 
)
-katenkak-
katenkak on Jul 21 2009, 11:44 AM said:
Hi everybody! I have a mouse strain lacking a gene. In tissues lysate derived from this mouse, there is a protein with increased expression compared to the wild type. When I add a chemical that compensate for the lack of the gene, the expression of the protein is downregulated. I am eager to know which transcription factor regulates an expression of the protein, but don't know how to do it. If I would wanted to check whether a given transcription factor binds to some promoter(s), I'd do Chip employing antibody against transription factor followed by PCR, but what to do in such sort of reversed situation? Many-many thanks for ideas! (I'll mention your help if get published in Nature )
)If you know the upregulated protein, do its promoter analysis through bioinformatics. (TF binding sites, evolutionary conservation thereof etc).
Then, make an intelligent and informed choice of transcription factors that you think may really be involved in the pathway, and do ChIP, reporter analysis and EMSAs for it.
-cellcounter-