I have a really basic question. Studying ChIP coupled with q-PCR or sequencing, I see different levels of a certain protein among a genomic region. I cannot really understand how can we have different protein levels. I thought that the binding of a protein in a region is bivalent-it occurs or not. But, as I can understand, we can have different concentration/quantity of protein bound to a region? And if this is the case, how in ChIP-qPCR we get finally DNA fragments, so how can we measure this binding from the quantity of fragments?
Protein binding to DNA is not bivalent. ChIP is enriching for DNA to which your protein of interest is bound, but that protein may bind certain sites throughout the genome more strongly and frequently than others. Stochiometric effects play a role, as do the strength of the binding motifs.
Some proteins bind very specifically to a given sequence, but most allow for some degeneracy in their binding sites. A strong site will be bound more frequently (and thus more highly enriched during ChIP) than a weaker site. Not just the presence, but the frequency of binding is what ChIP really measures.