Interpreting ChIP-qPCR or ChIP-seq

Question

[panagiotix]

Hi to all.

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?

Thank you very much

Answer 1

[Devon Ryan]

While a protein is either bound or not to a particular chromosome in a particular cell, you're not doing ChIP qPCR on single cells, but rather on a bulk of cells. Heck, even within a single cell you can have different amounts of binding due to the cell's ploidy.