Core Components of the Nuclear Pore Bind Distinct States of Chromatin and Contribute to Polycomb Repression

Mol Cell. 2020 Jan 2;77(1):67-81.e7. doi: 10.1016/j.molcel.2019.10.017. Epub 2019 Nov 26.


Interactions between the genome and the nuclear pore complex (NPC) have been implicated in multiple gene regulatory processes, but the underlying logic of these interactions remains poorly defined. Here, we report high-resolution chromatin binding maps of two core components of the NPC, Nup107 and Nup93, in Drosophila cells. Our investigation uncovered differential binding of these NPC subunits, where Nup107 preferentially targets active genes while Nup93 associates primarily with Polycomb-silenced regions. Comparison to Lamin-associated domains (LADs) revealed that NPC binding sites can be found within LADs, demonstrating a linear binding of the genome along the nuclear envelope. Importantly, we identified a functional role of Nup93 in silencing of Polycomb target genes and in spatial folding of Polycomb domains. Our findings lend to a model where different nuclear pores bind different types of chromatin via interactions with specific NPC sub-complexes, and a subset of Polycomb domains is stabilized by interactions with Nup93.

Keywords: Elys; Nup107; Nup93; Polycomb; chromatin; gene silencing; genome architecture; nuclear organization; nuclear pore; nucleoporin.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Aquaporins / metabolism
  • Binding Sites / physiology
  • Cell Line
  • Chromatin / metabolism*
  • Drosophila / metabolism
  • Drosophila Proteins / metabolism
  • Female
  • Gene Expression Regulation / physiology
  • Genome / physiology
  • Male
  • Nuclear Envelope / metabolism
  • Nuclear Pore / metabolism*
  • Nuclear Pore Complex Proteins / metabolism
  • Polycomb-Group Proteins / metabolism*


  • Aquaporins
  • Chromatin
  • Drosophila Proteins
  • Nuclear Pore Complex Proteins
  • Nup107 protein, Drosophila
  • Polycomb-Group Proteins