Nuclear Pore Complexes As Scaffolds For Genome Architecture And Epigenetic Maintenance

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Abstract: The Nuclear Pore Complex (NPC) is a nuclear envelope-embedded multi-component complex, which mediates transport of molecules between the nucleus and the cytoplasm. In addition to their classical function in transport, NPC components (Nups) have been implicated in transcriptional regulation via binding to the genome. Yet what regulatory steps of transcription are controlled by Nups and how chromatin-binding roles of Nups contribute to metazoan development is currently unclear. We identified the binding of multiple Nups to hundreds of promoters and enhancers in the Drosophila genome, and discovered a previously unreported role of the NPC in the formation of enhancer-promoter loops. Specifically, we identified Nup98 to be required for the formation of an enhancer-promoter loop at a gene activated by a developmental hormone ecdysone. Functionally, we found that the loss of Nup98-mediated enhancer-promoter loop affected the primed response to subsequent activation or transcriptional memory. Interestingly, ecdysone-regulated genes stably associated with nuclear pores before and after activation, suggesting that metazoan NPCs can be utilized as an organizing scaffold for genes awaiting future activation events. Together, these findings implicate Nups as a new class of architectural proteins for enhancers and suggest that stabilization of enhancer-promoter loops by nuclear pore binding constitutes a mechanism of epigenetic maintenance. We project that this function of the nuclear pore will be highly relevant to gene regulation during metazoan development. To be able to investigate the genome- organizing role of Nups in developmental gene regulation, we first plan to identify molecular determinants of Nup-mediated enhancer-promoter looping. Thus, in Aim 1, we will define which Nups and which other architectural proteins participate in the establishment of ecdysone- induced genomic loops. Additionally, we plan to identify DNA elements that are sufficient to tether to the NPC or that are necessary for loop stabilization. In Aim 2, we propose to define the relationship between formation of Nup-mediated enhancer-promoter loops and transcriptional activation and memory, by identifying chromatin changes that occur as a specific consequence of looping. Furthermore, we will examine the effect of Nups on maintenance of genomic loops in fly tissues during development and identify a comprehensive set of genomic contacts that are regulated by Nups. Together, these experiments are expected to expand our knowledge of the driving forces and principles of genome architecture, gene expression and nuclear pore biology.