Nuclear Pores provide a scaffold for induced enhancer promoter contacts

We found that in addition to promoters, multiple Nups bind enhancers and insulators in the Drosophila genome. We identified a functional role for Nup98 in mediating enhancer-promoter looping at ecdysone-inducible genes. These genes were found to be stably associated with nuclear pores before and after activation. Interestingly, although changing the levels of Nup98 disrupted induced enhancer-promoter contact, it did not affect transcriptional activation. Instead, loss of Nup98-mediated enhancer-promoter contact affected the primed response to subsequent transcriptional activation or transcriptional memory. In support of the enhancer-looping role, we found Nup98 to gain and retain physical interactions with several architectural proteins upon stimulation with ecdysone. Characterization of Nup98 occupancy by ChIP-Seq in drosophila embryonic S2 cells. Drosophila brains were also dissected from 3rd instar larvae and ChIP-Seq were performed using Nup93, Elys, Nup98, H3K27ac and H3K27m3 antibodies. Control S2 cells and Nup93 and Elys knockdown cells were used to test antibodies specificity.