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

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. Overall design: Massively Parallel Reporter Assays (MPRA) of variants linked via GWAS to skin disease in human keratinocytes to identify variants with increased potential for transcriptonal effects, and effects from differentiation. 8 samples of primary keratinocytes, 2-3 tissue donors and 2 plasmid sequencing samples. Cells were either harvested in progenitor growth conditions (D0), after three (D3) or six (D6) days of differentiation. The uploaded fastq files are the result of running the indicated umi_tools extract command.