Fig. 4: ARID1A activates Nfatc1 transcription at SE during proliferation-differentiation switching.
From: ARID1A safeguards the canalization of the cell fate decision during osteoclastogenesis
a Pseudotime trajectory colored by cell clusters. b PAGA graph showing trajectory colored by the timeline in upper and the proportion in the target cell cluster in lower. c Bar plot of the top 10 enriched KEGG pathways in cluster 4 between control and LysM-Cre;Arid1afl/f group. d Total H3K27Ac ChIP-seq signal in units of reads per million in enhancer regions for all enhancers in BMCs after RANKL-induction. e Venn diagram showing overlapping genes between ARID1A occupied, SE-associated genes with OC-associated DEGs after loss of Arid1a within cluster 4. f UMAP visualization of Nfatc1 expression in control and LysM-Cre;Arid1afl/fl group. g NFATc1 immunofluorescence and EdU visualization in RANKL-inducted BMCs from control and LysM-Cre;Arid1afl/fl mice. Yellow arrows indicate EdU+ NFATc1+ cells. Scale bar, 100 μm. h ARID1A, NFATc1, MMP9, and CTSK protein expressions in Nfatc1-overexpressed (OE) and control BMCs from control and LysM-Cre;Arid1afl/fl group after RANKL-induction. i Luciferase reporter activity driven by Nfatc1 promoter and enhancer elements. Gene tracks of H3K27Ac and ARID1A ChIP-seq occupancy at the super enhancer of Nfatc1 in RANKL-induced BMCs (top panel). Gray box indicates promoter region (Pro). Yellow boxes indicate the presentative enhancer regions upstream (E1) and downstream (E2 and E3). Data were normalized to Renilla internal control. n = 6 biologically independent samples. j 3C-qPCR analysis of interaction frequency percentage of the restriction fragments with the anchor point fixed near Nfatc1 promoter in 24 h RANKL-induced BMCs. The gray shadows highlight the regions containing E2 and E3 enhancer elements and the anchor point. n = 4 biologically independent samples. k Interaction frequency of the restriction fragments in E2, E3 with Nfatc1 promoter in BMCs from control and LysM-Cre;Arid1afl/fl mice with or without 24 h RANKL-induction. n = 3 biologically independent samples. Short-range ligation product used for normalizion for j, k. All data in this figure are represented as mean ± SD. One-way ANOVA with Dunnett’s multiple comparisons test for i, k. All experiments were performed in triplicates unless otherwise stated. Source data and exact p values are provided in the Source data file.
