Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts

Mol Cell. 2017 Apr 6;66(1):63-76.e6. doi: 10.1016/j.molcel.2017.02.020. Epub 2017 Mar 30.

Abstract

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

MeSH terms

  • Animals
  • Animals, Genetically Modified
  • Binding Sites
  • Cell Line
  • Chromatin / genetics
  • Chromatin / metabolism*
  • Drosophila Proteins / genetics
  • Drosophila Proteins / metabolism*
  • Drosophila melanogaster / drug effects
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / metabolism*
  • Ecdysone / pharmacology
  • Enhancer Elements, Genetic*
  • Genotype
  • Insulator Elements
  • Mutation
  • Nuclear Pore Complex Proteins / genetics
  • Nuclear Pore Complex Proteins / metabolism
  • Phenotype
  • Promoter Regions, Genetic*
  • Protein Binding
  • RNA Interference
  • Transcription, Genetic* / drug effects
  • Transcriptional Activation* / drug effects
  • Transfection

Substances

  • Chromatin
  • Drosophila Proteins
  • Nuclear Pore Complex Proteins
  • nuclear pore complex protein 98
  • Ecdysone