Y-complex nucleoporins independently contribute to nuclear pore assembly and gene regulation in neuronal progenitors

From their essential function in building up the nuclear pore complexes, nucleoporins have expanded roles beyond nuclear transport. Hence, their contribution to chromatin organization and gene expression has set them as critical players in development and pathologies. We previously reported that Nup133 and Seh1, two components of the Y-complex subunit of the nuclear pore scaffold, are dispensable in mouse embryonic stem cells but required for their survival during neuroectodermal differentiation. Here, a transcriptomic analysis revealed that Nup133 regulates a subset of genes at early stages of neuroectodermal differentiation, including Lhx1 and Nup210L, encoding a newly validated nucleoporin. These genes were also misregulated in Nup133?Mid neuronal progenitors, in which NPC basket assembly is impaired, as previously observed in pluripotent cells. However, a four-fold reduction of Nup133, despite affecting basket assembly, is not sufficient to alter Nup210L and Lhx1 regulation. Finally, these two genes are misregulated in Seh1-deficient progenitors that only show a mild decrease in NPC density. Together these data reveal a shared function of Y-complex nucleoporins in gene regulation during neuroectodermal differentiation. Overall design: We compared the transcriptome of WT and Nup133-/- mESCs at the pluripotent state and after 2 or 3 days of differentiation towards neuroectodermal lineage. We therefore used cell lines from two distinct genetic background, namely the HM1 control cell line (Selfridge et al., 1992, PMID: 1440055) and its CRISPR/Cas9-edited Nup133-/- derivatives (#14 and #19), and the blastocyst-derived control (#1A4) and Nup133-/- (merm, #319) mESC lines (cell lines described in Souquet et al., 2018 - PMID: 30428363).