Genome-wide association studies indicate that >90% of disease-susceptibility regions reside in non-protein coding regions of the genome. Identification of all genetic elements contributing to proper skin development remains an ongoing challenge and is crucial to understand the complex regulation in (diseased) skin. Long non-coding RNAs (lncRNAs) are a major component of the non-coding genome and their role as important gene regulators is emerging. In our research, we identified 2,263 lncRNAs expressed in human epidermal biopsies and, with only a few functional epidermal lncRNAs currently described, we hypothesized that additional lncRNAs contribute to epidermis formation. Hence, we employed a comprehensive CRISPR interference (CRISPRi) screen of all epidermally expressed lncRNAs in human progenitor keratinocytes to identify functional lncRNAs regulating their proliferation. Screen results were benchmarked against TINCR, a lncRNA known to be involved in epidermal homeostasis, leading to the identification (FDR < 0.01) of 13 novel lncRNAs impacting epidermal progenitor renewal.  Deep characterization of a top hit using RNA interference, identified a lncRNA required for progenitor proliferation, clonogenicity and cell cycle progression, as well as for stratification, differentiation and epidermal barrier formation during organotypic epidermis formation. We termed this lncRNA progenitor renewal associated noncoding RNA (PRANCR). Mechanistically, PRANCR regulates expression of late cell cycle genes by controlling the DREAM-E2F4 transcription complex. In addition, PRANCR regulates mRNA isoform splicing of disease-relevant epidermal genes, e.g. the Extra Domain A-containing exon of fibronectin-1 (FN1), which is crucial for replication and migration of keratinocytes during wound healing. Our study provides a systemic identification of functional lncRNAs in human cells and tissues and serves as a foundation of understanding their role in somatic tissue homeostasis and disease.

A CRISPR-interference screen identifies PRANCR and other novel long non-coding RNAs controlling human epidermis formation