CPSF controls PAS selection and epidermal differentiation

Alternative polyadenylation (APA) is a regulatory mechanism that controls gene expression level and function through the usage of different transcription termination sites, but how APA is regulated to influence epidermal tissue differentiation remains under-characterized. Leveraging 3'READS+, we identified prevalent APA in keratinocytes. We further identified a high-confidence list of genes that alters their usages of polyadenylation site (PAS) during keratinocyte differentiation. To begin to understand the mechanisms that modulates PAS selection within a given gene, we identified that the expression of the Cleavage and Polyadenylation Specificity Factor (CPSF) complex is down regulated during keratinocyte differentiation. Suppression of CPSF using RNAi or CRISPRi strongly impaired epidermal regeneration with upregulation of terminal differentiation marker gene expression. Mechanistically, we identified that CPSF suppression decreased the usage of the GRHL3 proximal PAS and upregulated full-length GRHL3 mRNA production. Knockdown of GRHL3 in the context of CPSFi partially restored differentiation marker gene expression. We also found CPSF interacts with RNA-binding proteins to control PAS usage. Thus, our data suggest a model where CPSF binding preference and PAS choices regulate epidermal terminal differentiation. Overall design: We examined alternative polyadenylation by 3'READS+ in undifferentiated and differentiated keratinocytes with two biological replicates each, as well as in CPSF1 siRNA knock down codition. To check gene expression in epidermal differentiation, we performed RNA-seq in undifferentiated and differentiated keratinocytes with three biological replicates each. To check whether the CPSF complex regulates keratinocyte gene expression, we further performed RNA-seq in control and CPSF1 siRNA knock down conditions with two replicates each, and RNA-seq in control and CPSF1 CRISPRi knock down conditions with two and three biologial replicats respectively.