Fig 2: Working model.NUP98 and RAE1 support epidermal progenitor maintenance through binding to chromatin near the transcription start sites of key target genes such as the epigenetic repressor DNMT1. NUP98 and RAE1’s roles in progenitor maintenance depend on two factors: high expression and HDAC activity. The high expression of NUP98 and RAE1 provides the chromatin-binding pool, in addition to their nuclear-pore incorporation; HDAC activity supports NUP98’s binding on chromatin near the TSSs of key target genes, antagonizing the nucleolar localization of NUP98 and RAE1.

Fig 3: NUP98 or RAE1 knockdown impairs progenitors’ regenerative capacity.a, b RT-qPCR showing knockdown efficiency of 3 independent shRNA targeting NUP98 or RAE1 (one-way ANOVA with post-hoc test, N = 3, data are represented as mean ± standard deviation). c–f Representative images and quantification of clonogenicity assay comparing keratinocytes with NUP98 or RAE1 knockdown versus control (one-way ANOVA with post-hoc test, N = 3, quantification data are represented as mean ± standard deviation.) g Representative images of competition assay in epidermal tissue regeneration. An equal number of keratinocytes expressing DsRed or GFP were mixed seeded onto human dermis. GFP-expressing keratinocytes co-express control shRNA, and DsRed-expressing keratinocytes co-express control shRNA or shRNA targeting NUP98 or RAE1 (scale bar = 125 µm). h Quantification of DsRed or GFP-expressing keratinocytes in the basal layer of the regenerated epidermis, data are represented as mean ± standard deviation. i Venn diagram showing the overlap of NUP98 and RAE1 knockdown differentially expressed genes (Fisher’s exact test, p = 1 × 10-321). j Heatmap showing the relative expression of shared genes with NUP98 or RAE1 knockdown. k Top three gene ontology (GO) terms for the upregulated or downregulated genes shared by NUP98 and RAE1 knockdown, identified by RNA-seq analyses.

Fig 4: NUP98 and RAE1’s nucleolar localization is balanced between HDAC and HAT activities.a Co-immunostaining of NUP98 and nucleolus marker FIB in keratinocytes treated with HDAC inhibitor, ROM, and/or the HAT inhibitor A485 (scale bar = 25 µm). b quantification of NUP98 nucleolus enrichment in these treatment conditions (one-way ANOVA with post-hoc test, N = 5, data are represented as mean ± standard deviation). c Co-immunostaining of RAE1 and the nucleolus marker FIB in keratinocytes treated with HDAC inhibitor, ROM, and/or the HAT inhibitor A485 (scale bar = 25 µm). d quantification of RAE1 nucleolus enrichment among these conditions (one-way ANOVA with post-hoc test, N = 5, data are represented as mean ± standard deviation).

Fig 5: NUP98 binds near the TSSs of key regulators in progenitor maintenance.a–d Summit-centered heatmaps and average diagrams comparing NUP98 ChIP enrichment between the progenitor state (UD) and the differentiation state (DF). e–g Pie charts showing the distribution of the NUP98 ChIP-seq peaks, based on their distances to the nearest Transcriptional Start Sites (TSSs). h Average diagram comparing NUP98 ChIP-seq enrichment near the transcription start and end sites of the target genes. i Top Gene Ontology (GO) terms of the nearest genes associated with NUP98 ChIP-seq peaks. j Heatmap showing the 101 genes, featuring NUP98 ChIP-seq enrichment and are significantly changed with NUP98 knockdown. Relative NUP98 ChIP enrichment in UD and DF associated with these gene, and their relative expression with NUP98 or RAE1 knockdown, are included for each of these genes side by side. k–m Browser track examples of NUP98 ChIP-seq enrichment, comparing UD vs. DF. n, o qRT-PCR validation of representative target genes with NUP98 or RAE1 knockdown (one-way ANOVA with post-hoc test, N = 3 biological replicates, data are represented as mean ± standard deviation). p–s Western blot and quantification comparing DNMT1 protein levels with NUP98 or RAE1 knockdown, with Lamin used as the loading control (one-way ANOVA with post-hoc test, N = 3, quantification data are represented as mean ± standard deviation).