NUP98 and RAE1 sustain progenitor self-renewal programs downstream to HDAC activity to antagonize nucleolar targeting

Here we determine the target gene sets controlled by NUP98 and RAE1 in maintaining the undifferentiated state of primary human keratinocytes via HDAC activity. We use primary human keratinocytes pooled from 6 donors. RNA-seq data comparing keratinocytes with NUP98 knockdown or RAE1 knockdown (3 independent shRNAs for each gene) vs their controls (2 independent control shRNAs for each gene) were generated. To determine NUP98's binding sites on the genome, we performed NUP98 ChIP-seq im undifferentiated and differentiated keratinocytes (day 4, with 1.2mM CaCl2). HDAC inhibition RNA-seq data were generated comparing DMSO treated cells to SAHA (10 uM) or romidepsin (100nM) treated cells for 24 hrs. HDAC1 ChIP-seq was done in untreated keratinocytes as well as in NUP98-knockdown versus control (2 independent shRNA and 2 independent control shRNA). To determine if HDAC inhibition affects NUP98 chromatin binding, NUP98 ChIP date on DMSO, SAHA, and romidepsin treated cells were also generated. We use primary human keratinocytes pooled from 6 donors. To determine NUP98 and HDAC1 binding sites on the genome, we performed NUP98 and HDAC1 ChIP-seq in differentiated keratinocytes (day 4, with 1.2mM CaCl2) . To determine RAE1 binding sites on the genome, we performed expressed and HA tagged RAE1 and used an HA antibody for ChIP.