Molecular Cell
Volume 66, Issue 1, 6 April 2017, Pages 63-76.e6
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Article
Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts

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Highlights

  • Nuclear pore proteins (Nups) bind promoters and enhancers in Drosophila cells and tissues

  • Nup98 mediates enhancer-promoter looping of inducible genes

  • Inducible genes stably associate with nuclear pores in their silent and active states

  • Nup98 gains and retains interactions with architectural proteins upon induction

Summary

Nuclear pore complex components (Nups) have been implicated in transcriptional regulation, yet what regulatory steps are controlled by metazoan Nups remains unclear. We identified the presence of multiple Nups at promoters, enhancers, and insulators in the Drosophila genome. In line with this binding, we uncovered 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. Although changing levels of Nup98 disrupted enhancer-promoter contacts, it did not affect ongoing transcription but instead compromised subsequent transcriptional activation or transcriptional memory. In support of the enhancer-looping role, we found Nup98 to gain and retain physical interactions with architectural proteins upon stimulation with ecdysone. Together, our data identify Nups as a class of architectural proteins for enhancers and supports a model in which animal genomes use the nuclear pore as an organizing scaffold for inducible poised genes.

Keywords

nuclear pore complex
nucleoporin
Nup98
transcription
transcriptional memory
enhancer
looping
genome architecture
nuclear organization
poised genes

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