FAIRE vs H3K27Ac ChIP

Question

[asharmatelome]

Hi, I am using two techniques to look for open chromatin FAIRE and H3K27Ac. I would like to send both libraries for Next-gen seq.. However, during initial q-PCR level FAIRE is giving me expected results (opening and closing of enhancer region in control vs treatment) but H3K27Ac ChIP-qPCR is not giving me significant difference for that particular enhance in control vs treatment. I am getting ~ 10 fold increase in signal compare to my Input which suggest that ChIP worked. I am wondering how many time these two techniques were compared for same experimental setting? Anyone?

Thanks,
Ankur

Answer 1

[dariober]

I don't know how a typical (if there's a typical) H3K27Ac ChIP-Seq pull down looks like. However, FAIRE and ChIP-seq are very different methods. With FAIRE you expect to retain and sequence everything that is not bound by proteins. With ChIP-Seq you sequence what is bound by your antibody (with a lot of hand-waving as these techniques are far from perfect). So I'm not that surprised by your inconsistent results, but I know nothing about your control regions...

[asharmatelome]

Thanks Dariober, my control regions are ChIP negative region for mouse genome (I am using mouse cell lines) and I don't see any enrichment in ChIPed faction for this region however some of the expected enhancers are enriched in ChIP.