Supplemental Material: Allele-specific expression reveals genetic drivers of tissue regeneration in mice

In adult mammals, skin wounds typically heal by scarring rather than through regeneration. In contrast, “super-healer” MRL mice have the unusual ability to regenerate ear punch wounds, yet the molecular basis for this regeneration remains elusive. Here, in hybrid crosses between MRL and non-regenerating mice, we use allele-specific gene expression to identify cis-regulatory variation associated with ear regeneration. Analyzing three major wound cell populations, we identified extensive strain- and tissue- specific cis-regulatory divergence associated with differences in healing outcomes. Genes with cis-regulatory differences specifically in fibroblasts were associated with wound healing phenotypes and pathways, and were enriched near genetic markers associated with ear-healing in a genetic cross. We further demonstrated that one of these genes, CFH, could be applied ectopically to accelerate wound repair and induce regeneration in typically fibrotic wounds. Through single-cell RNA-seq, we observed that CFH treatment strongly dramatically reduced immune cell recruitment to wounds, suggesting a potential mechanism for CFH’s effect. In support of this, CFH strongly down-regulated the neutrophil chemoattractant CXCL2, and chemical inhibition of CXCL2’s receptor in dorsal wounds mimicked the regenerative phenotype of MRL ear wounds. Overall, our results provide insight into the molecular drivers of regeneration in MRL mice with potential clinical implications.