Nuclear pore complexes (NPCs) allow for nucleocytoplasmic transport through the nuclear envelope. Mutations in nucleoporin (Nup) genes are associated with rare diseases that affect several discrete tissues, even though NPC proteins are expressed in nearly all cell types. Investigation of Nup functions has revealed additional roles for the NPC in chromatin organisation and gene expression, but in many cases, it remains unclear whether the regulatory functions of Nups are an indirect consequence of their structural role in NPC assembly and integrity. Valérie Doye and colleagues previously reported that mouse embryonic stem cells (mESCs) lacking Nup133 or Seh1, components of the NPC Y-complex, show impaired capacity for neuroectodermal differentiation, but exhibit differing NPC alterations. This suggests that the development of neuronal progenitors depends on gene regulation by these Nups separately from NPC assembly. Here (Orniacki et al., 2023), the authors seek to identify key genes misregulated in differentiatingmESCs and find that, in the absence of Nup133 or Seh1, Lhx1 and Nup210l are significantly de-repressed during neuroectodermal differentiation. Depletion of Nup133 or Seh1 in the early stages of differentiation results in the rapid upregulation of Nup210l, which can be uncoupled from the various roles of these two Nups in NPC integrity. These findings further demonstrate the complex multifunctionality of Nups in development that might also be pertinent for understanding Nup-associated disease mechanisms.