Extended Data Fig. 4: RXR and RAR family members are expressed in proximity to corpses during apoptotic regression.

a, Representative histograms of fragment lengths in base pairs (bp) detected per biological replicate for each hair cycle stage examined by ATAC-seq. Nucleosome-free, mono- and di-nucleosome peaks were identifiable for all replicates analysed. b, Principal component analysis on reads mapped to peaks separates ATAC-seq biological replicates by hair cycle stage; n = 2 (anagen) and n = 6 (catagen) c, Pearson correlation (R²) values for reads mapped to peaks across replicates. d, Bar graph of peaks partitioning across the genome. e, Heatmap showing all peaks with significantly altered accessibility between anagen and catagen replicates. Accessibility signal for pooled replicate samples is normalized for fraction of reads in peaks, and scaled to reads per genome coverage (RPGC) (colourbar legend, right). Each row corresponds to a detected peak, centered and extended +/− 1 kb. Peaks are clustered based on differential accessibility, and summarized as the mean accessibility signal per region in a blue line (peaks gaining accessibility in catagen) or a pink line (peaks losing accessibility in catagen) in the graph at top. f, Motif enrichment analysis of the 13,664 peaks losing accessibility in catagen replicates. See Supplementary Table 3 for full list. Quantification via Binomial test (two-tailed, confidence interval 95%). g, Schematic depicting retinoid X receptor (RXR) and retinoic acid receptor (RAR) transcription factor signaling. h, Dot plot summarizing non-steroidal nuclear hormone receptor family expression across the hair cycle from single cell transcriptomic data. i, j, Sagittal skin sections of RXRα⁺ cells (i) and RARγ⁺ cells (j) within wild type skin from the end of anagen growth phase (AnaVI) throughout catagen (Cat). Dashed line denotes epithelial-dermal border; asterisk denotes TUNEL⁺ de-nuclearization of hair shaft lineages as part of differentiation. Pcad, p-cadherin. Scale bar 15 μm. Quantifications, inset. RXRα+: n = 35 HFs (AnaVI), 58 HFs (CatII), 62 HFs (CatIV-VI), 49 HFs (CatVII-VIII) and 45 HFs (Telo) across 8 mice. RARγ+: n = 21 HFs (AnaVI), 17 HFs (CatII), 58 HFs (CatIV-VI), 53 HFs (CatVII-VIII) and 10 HFs (Telo) across 6 mice. Quantifications, pairwise independent Student’s T-Tests (2-sided), p-values indicated. n.s. not significant (p > 0.05). Data as box-and-whisker plots; box: first-to-third quartiles and median, whiskers 1.5X inter-quartile range. More details on statistics and reproducibility can be found in the Methods section.

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