why location of binding sites are different while human sequence is the same?

Question

[na.cna30]

Hello:

I have a basic question:

why location of binding sites like enhancers are depended on cell line? considering that human map like HG19 is fixed in UCSC, but histone signals which represent location of binding sites are different according to cell lines?

thanks.

Answer 1

[Emily]

I suggest you read up on epigenetics and cell differentiation. Different cell types serve different functions, therefore need different genes to be expressed. To do this, epigenetic marks differ between the cell types, resulting in different binding of transcription factors. This will cause gross differences.

Smaller differences in sites will be caused by technique. We find TFBSs and locations of histone modifications by ChIP-Seq. Proteins are covalently linked to the DNA, the DNA is cut into small fragments at random, we pull out our histone mod/TF with an antibody, then we clean and sequence the DNA and map it onto the genome. Since the DNA cutting is random, this means that we could have quite long or short tails on our DNA, making the edges of our binding sites necessarily fuzzy. This means that two identical experiments looking at an identical TFBS will still have peaks that don't match exactly.