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I am writing a project proposal and I have to talk about this problem: how to identify the genes that distal enhancers pair?

I am really new to this topic and I don't know what it is all about. I have been searching the literature but I did not find anything useful. Can someone explain to me what it is all about? Maybe suggest some papers to me.

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  • $\begingroup$ To make sure I understand your question right: You want to know how distal enhancers of genes are identified? $\endgroup$ – Chris Aug 26 '14 at 9:10
  • $\begingroup$ @Chris Yes, and how enhancers regulate distal genes. Thanks. $\endgroup$ – DavideChicco.it Aug 26 '14 at 9:13
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Check this technique called Chromosome Conformation Capture (3C). Its variants exist such as 4C, Hi-C etc.

Basically, the principle of this technique is based on the physical interaction between the enhancer and promoter that is bridged by a transcriptional modulator(protein).

  1. The chromatin is crosslinked
  2. DNA is sheared
  3. The protein is pulled down (Optional)
  4. The fragments of the promoter and enhancer are ligated together and then sequencing/qRTPCR is done.

Sequencing (low throughput- sanger) can be used to identify enhancers of a given promoter. qRTPCR can be used to quantify the strength of the association.

What I just said is not a high throughput technique. Hi-C is high throughput variant of 3C. See the protocol here.

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