As we know we have polyploidy cell lines with more chromosomes,  and maybe this situation makes the nuclei more condense. According to the principles of 4Cseq we try to have a snapshot of interaction of different parts of one special chromosome and particular locus. Because of this reason we try to prevent or decrease interaction between different chromosomes.

Is it possible that high density of nuclei increase the chance of inter chromosomes interactions?

If yes, how we can decrease it?

Thanks

Reza