Fig. 7: Transcriptional de-repression is a functional component of wound memory.
From: Tissue memory relies on stem cell priming in distal undamaged areas
a, Epidermal whole mounts of H2AK119ub in INFU at 0w and 8w pw1, 1w pw1 and 1w pw2, in distal memory area (5 mm from wound bed). b, Setting for PRT4165 treatment in Lrig1 GL mice: day 0, genetic labelling through 4-Hydroxytamoxifen (4OHT); day 7-9-11, PRT4165/vehicle treatments; day 11, 6 h after the last treatment scRNA-seq, ATAC–seq or a full-thickness injury; day 18 (1w pw1), histology. c, Epidermal whole mounts of Lrig1 GL tdTomato+-treated cells. d,e, scRNA-seq data from Lrig1 GL-treated cells. d, UMAP of cells coloured by cluster. e, Heat map of known memory GO terms. Gene expression is shown per cluster as ratio between PRT4165- and vehicle-treated cells. f–k, ATAC–seq of sorted Lrig1 GL upper-HF cells (Sca-1+) from PRT4165- and vehicle-treated skin. f, Genomic loci gained after PRT4165 treatment. g, Density plots of ATAC–seq signals ±1 kb of peaks (logFC > 0.5, P < 0.05) (top) and heat map of the signal score of individual peaks (bottom). h, Venn diagram showing the ATAC–seq peaks gained in PRT4165-treated versus vehicle-treated (red). i,j, Analysis of genes associated with gained peaks in PRT4165-treated versus vehicle-treated. i, Intersection between these genes and the genes associated to distal memory peaks. Random permutation p-value (P) is shown. j, GO analysis, plotted as −log10 of adjusted p-value (AdjP). Dashed line underlines significance. k, Transcription factor (TF) motifs enrichment for PRT4165 gained peaks (to vehicle), based on de novo motif discovery. Ranking of motifs with a match score of >0.8 to a known motif. l, 3D surface plots of Lrig1 GL cells from HF whole mounts. Dashed line represents the IFE–HF boundary while arrows the IFE exit. m, Quantification (left) and images (right) of ex vivo assay of treated Lrig1 GL skin (red channel). n = 10 explants. n, Glut1 quantification (left) and INFU whole mounts (right) of treated epidermis. n = 6 mice. P-value from a two-tailed t-test, if not differently indicated. Data are mean ± s.d. Scale bars: 50 μm (a, l, m and n); 1 mm (c). scRNA-seq (d and e) and ATAC–seq (f–k) data are the integration of two independent experiments, each of them based on four and two biological replicates, respectively.
