ZNF750 is a p63 target gene that induces KLF4 to drive terminal epidermal differentiation

Abstract

Disrupted epidermal differentiation characterizes numerous diseases that impact >25% of the population. In a search for dominant mediators of differentiation, we defined a requirement for ZNF750 in terminal epidermal differentiation. ZNF750 controlled genes mutated in numerous human skin diseases, including FLG, LOR, LCE3B, ALOXE3, and SPINK5. ZNF750 induced progenitor differentiation via an evolutionarily conserved C2H2 zinc finger motif. The epidermal master regulator, p63, bound the ZNF750 promoter and was necessary for its induction. ZNF750 restored differentiation to p63-deficient tissue, suggesting that it acts downstream of p63. A search for functionally important ZNF750 targets via analysis of ZNF750-regulated genes identified KLF4, a transcription factor that activates late epidermal differentiation. ZNF750 binds to KLF4 at multiple sites flanking the transcriptional start site and controls its expression. ZNF750 thus directly links a tissue-specifying factor, p63, to an effector of terminal differentiation, KLF4, and represents a potential future target for disorders of this process.

Figure 1

ZNF570 is required for terminal differentiation. (A) Differentiation gene induction heatmap on day 3 of calcium treated keratinocytes (+Ca2+) to induce differentiation as compared to undifferentiated sub confluent control keratinocytes (-Ca2+). (B) ZNF750 mRNA induction during calcium-induced differentiation in vitro [ordinate is log₁₀ scale]. Data show standard error of the mean (SEM). (C) ZNF750 protein induction during calcium-induced differentiation in vitro. (D) Effects of siRNA-mediated ZNF750 depletion (ZNF750i) versus scrambled control (CTL) on terminal differentiation proteins in regenerated organotypic human epidermal tissue; loricrin [LOR; green] and filaggrin [FLG; red], epidermal basement membrane is noted with dashed lines (scale bar=25μm). (E) Terminal differentiation gene mRNA quantitation in epidermal tissue with two independent ZNF750 siRNAs vs. scrambled control. Data show standard error of the mean (SEM). N=3. See also Figure S1.

Figure 2

An evolutionarily conserved amino terminal C2H2 zinc finger motif is required for ZNF750-driven terminal differentiation. (A) Induction of terminal differentiation genes in undifferentiated sub confluent cells requires an intact ZNF750 amino terminus. Fold mRNA induction quantified over undifferentiated control cells receiving vector control (CTL). Data shown SEM, n=3. (B) A C2H2 sequence in the evolutionarily conserved ZNF750 amino-terminus. (C) C2H2 sequence requirement in ZNF750-driven differentiation. Differentiation gene expression is shown with expression of full-length ZNF750 with point mutation in the amino-terminal C2H2 motif of either both cysteines (C2 Mut), both histidines (H2 Mut), all four residues (C2H2 Mut) or wild-type full-length control in undifferentiated human keratinocytes. Data shown SEM, n=3. See also Figure S2.

Figure 3

ZNF750 is a p63-dependent gene and rescues terminal differentiation gene expression in p63-deficient tissue. (A) ZNF750 gene locus with canonical p63 binding sequence noted in the promoter -0.5kb upstream of the transcriptional start site (TSS). (B) p63 chromatin immunoprecipitation at the ZNF750 promoter in differentiated keratinocytes with p63 depletion [p63i] versus scrambled siRNA control [CTL] to verify specificity. Data show mean with SEM. (C) Reduction in ZNF750 mRNA with p63 depletion at day 3 of calcium-induced differentiation in vitro; siRNA to p63 (p63i) and scrambled siRNA control (CTL). Data show SEM. (D) Reduction in ZNF750 protein with p63 depletion. (E) ZNF750 rescues loss of terminal differentiation gene expression due to p63 deficiency. mRNA quantification in tissue; p63i tissue is also depleted of p53 to bypass the growth arrest that occurs with loss of p63 alone. Data show SEM (F) Protein expression in tissue quantified in E. Note filaggrin protein expression in lower epidermis with ZNF750 (white arrowheads), scale bar= 30μm. See also Figure S3.

Fig. 4

ZNF750 regulates KLF4 to control terminal epidermal differentiation. (A) Venn diagram (left) illustrating overlap between ZNF750-dependent genes and differentiation genes. The blue circle (Differentiation/ CTL: 3,304 genes) represents all the genes that change significantly by >2-fold during epidermal differentiation. The yellow circle (Differentiation/ZNF750i: 1,978 genes) represents the genes that change significantly >2-fold when ZNF750 is knocked down during differentiation compared to control differentiated cells. The overlap (878 genes; green) shows ZNF750-regulated epidermal differentiation genes. Heat map (middle) of the overlap showing epidermal differentiation regulated genes affected by ZNF750 depletion during differentiation. CTL and ZNF750i represent heatmaps generated from control and ZNF750i cells induced to differentiate. Heatmaps were normalized to undifferentiated control cells (red [induced] and blue [repressed]), log₂ based scale. Gene Ontology terms (right) of ZNF750-dependent genes (p-values represent Bonferroni- corrected EASE score). (B) Consensus mouse KLF4 binding motif (left panel) and consensus KLF4 binding motif (right panel) found informatically enriched in the promoter regions of ZNF750-dependent genes. (C) 629 of the 1978 ZNF750 dependent genes contain consensus KLF4 binding sites in their respective promoter regions. (D) Venn diagram illustrating overlap between changes identified with KLF4 and ZNF750 depletion in primary keratinocytes induced to differentiate with calcium. These data were derived by first determining the significantly changed genes between KLF4i and control cells during differentiation (3,138 genes) and overlapping them to the significantly changed genes between ZNF750i and control cells during differentiation (1,978 genes). (E) ChIP demonstrating ZNF750 binding to the regions of the KLF4 gene that flank the transcription start site (TSS) in differentiating epidermal cells. ZNF750i versus scrambled control (CTLi) knockdown represent specificity controls. Data show mean with SEM. (F) ZNF750 depletion impairs KLF4 induction in differentiating epidermal cells. Data show SEM (G) Ectopic expression of full length ZNF750 (ZNF750 FL), but not the C2H2 ZNF750 mutant or lacZ control (CTL), induces KLF4 in undifferentiated epidermal cells. Data show SEM. (H) Proposed model for epidermal differentiation. In this model, p63 induces the expression of ZNF750 during differentiation (solid arrow) as well as other factors necessary for differentiation (dashed arrow). ZNF750 induces differentiation in part by transcriptionally activating KLF4 (solid arrows). ZNF750 may also regulate other factors necessary for differentiation (dashed arrows). KLF4 can directly bind to differentiation gene promoters to activate terminal differentiation genes. See also Figure S4.