Compendium of Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis [crispr_flow]

Identifying the regulatory noncoding single nucleotide variants (SNVs) linked to polygenic disease risk, the transcription factors (TFs) they bind, and the target genes they dysregulate is a current focus in many tissues. Massively parallel reporter gene analysis (MPRA) of 3,451 SNVs linked to risk for prevalent human skin diseases identified 355 differentially active SNVs (daSNVs). daSNV target gene analysis, including genomic editing at three loci, highlighted dysregulated epidermal differentiation as a common pathomechanism. CRISPR knockout screens of 1,782 human TFs identified 108 TFs essential for epidermal homeostasis, validating new roles for ZNF217, CXXC1, FOXJ2, IRX2 and NRF1. Population sampling CUT&RUN from 310 samples of 27 homeostatic TFs across differentiation identified allele-specific binding differences enriched near epidermal homeostasis and monogenic skin disease genes, with prominent representation of SP/KLF and AP-1/2 family TFs. This resource indicates that dysregulated differentiation underlies pathogenic risk for diverse polygenic skin diseases. Guide RNA sequencing of CRISPR-flow samples, for a library targetting all transcription factors and sorting on the early keratinocyte differentiation marker KRT10. 20 samples of primary keratinocytes, 2 tissue donors (biorep*), two technical replicates (batch*), four sorting states on KRT10 (unsorted, low, medium, high) and a plasmid sequencing sample. Cells were either harvested in progenitor growth conditions (Prog) or after four days of differentiation (Day 4).