Extended Data Fig. 1: A distal enhancer regulates RANKL gene expression in arthritic SFs.

a, The expression pattern of representative cell-type marker genes in the CIA synovial cells (n = 2,160) in the UMAP visualization. The feature plots of the expression distribution of the major cell-type marker genes corresponding to the assigned cell types shown in (Fig. 1a). b, c, UMAP plots and unsupervised clustering of the synovial cells of individuals with RA (b) dbGaP Study Accession: phs001529.v1.p1, n = 19,599 cells; (c) ImmPort Accession: SDY998, n = 9,553 cells) colored by cluster. The violin plots on the right sides show the expression of the known SF marker genes. d, UMAP plot of the integrated SFs (n = 11,188 cells) from RA. Eight clusters (F1-F8) identified through unsupervised graph-based clustering are shown in color. Violin plots show the expression of selected genes in the SF sub-clusters. e, The sequence similarity of E1-E5 between humans and other vertebrates analyzed by the ECR Browser. The homologous sequence regions of E1-E5 in the mouse genome are indicated by arrows. f, Epigenomic analyses at the Tnfsf11 locus (mm9) in osteoblasts (vitamin D₃ stimulation followed by H3K27ac ChIP–seq and vitamin D receptor (VDR) ChIP–seq (GSE54782)), in T cells (anti-CD3/CD28 antibody stimulation followed by H3K27ac ChIP–seq (GSE123198)), in B cells (IL-2/IL-4/IL-5/CD40L stimulation followed by H3K27ac ChIP–seq (GSE145951)), in cardiac fibroblasts (TGFβ stimulation followed by H3K27ac ChIP–seq (GSE155882)), in arthritic SFs (TNF stimulation followed by ATAC–seq, PRJNA643827)). g, h, The expression levels of Tnfsf11 mRNA in arthritic SFs (WT: control, n = 3; stimulation, n = 2; E3-KO: control: n = 2; stimulation, n = 2) and lymphocytes (WT: control, n = 2; stimulation, n = 3; E3-KO: control: n = 2; stimulation, n = 4). Data were expressed as mean ± s.e.m. P values were determined by two-way ANOVA analysis followed by Turkey’s post hoc test.

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