I'm doing a 3C analysis shown in the picture linked and attached below with the Bait fragments labeled and the target fragments that will be tested for interaction with the bait labeled with numbers. The picture shows two possible 3c maps based on two different restriction enzyme digests of the same region.
https://ibb.co/4F2DKPS
A, B, C, and D are regions we are considering for analysis in the future to determine if they interact with each other and with the target fragments.
Assuming we can find restriction enzymes that can digest and separate the regions shown is it possible to test between the fragments as shown for interaction or are some of them too small/too close together?
In short, I'd suspect the target regions are simply too close to the baits to detect an enrichment of interaction over background. Anything less than 10kb away from the bait region is likely to interact with bait frequently enough by chance that you probably won't be able to discern a specific interaction peak. Ideally, you would like to see the 3C signal drop down to some background level as you get farther away from the bait before you get to the specific interaction target region. Take a look at Fig 2 of this paper (https://www.nature.com/articles/nmeth823) for an example of what this would look like and note that they don't see the interaction signal get down to background until 20kb-40kb away from the bait. I suspose you could try to see how quickly the random interaction signal drops away for your region but you should probably do a quick cost-benefit analysis for that in your head before taking that plunge. Good luck!