Nuclear Pore Complexes As Scaffolds For Genome Architecture And Epigenetic Maintenance

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.

Grant Number: 5R01GM124143-09
NIH Institute/Center: NIH
Principal Investigator: Maya Capelson