Fig. 3
Transcriptome characteristics and chromatin accessibility landscape of BMSCs from HFD-fed mice. a Volcano plot showing the expression levels of differentially expressed genes from the BMSCs of HFD-fed mice compared to those from control ND-fed mice. b Heatmap showing the downregulated expression of osteogenesis-related genes and upregulated expression of adipogenesis-related genes and senescent genes in BMSCs from HFD-fed mice. c Bubble plot of the Gene Ontology (GO) annotation terms enriched in differentially expressed genes in the BMSCs. Terms related to bone development are bolded and highlighted in red. d GSEA showing the upregulated expression of senescence-related genes in the BMSCs of HFD-fed mice. e, f The expression of the proinflammatory genes IL6 and IL1β in BMSCs from HFD-fed mice and ND-fed mice was detected by RT‒qPCR (e) and ELISA (f), respectively. The data were shown as the mean ± SEM. g Volcano plot showing ATAC-seq peaks. Differentially opened/closed peaks are indicated in red/blue for BMSCs from HFD-fed mice compared to those from ND-fed mice as the control. h Gene Ontology (GO) analysis of differentially accessible ATAC-seq peaks. Terms related to bone development, cell proliferation, and differentiation are bolded and highlighted in red. i Distribution of the genomic features of upregulated, downregulated, and stable ATAC-seq peaks in BMSCs from HFD-fed mice compared to those from ND-fed mice. j The differences in chromatin accessibility (ATAC-seq) at the promoter in the HFD group were generally consistent with the differences in expression (RNA-seq). k Motif analysis showed that the chromatin accessibility of 24 transcription factor motifs was upregulated, while that of 39 chromatin-binding factor motifs was downregulated in the BMSCs of HFD-fed mice. RNA-seq data revealed 15 transcription factors with differential expression, including Vdr, Hoxb9, Gsc, Hoxc5, Klf4, and Arnt2. After combining the RNA-seq data with the results of motif analysis, we found that there was only one factor, VDR, whose expression and chromatin accessibility to the motif were downregulated (padj < 0.1). l Relative chromatin accessibility around VDR ChIP-seq peaks (GSE79813) ± 2 kb. m Browser tracks showing downregulated chromatin accessibility at the VDR ChIP-seq peak in BMSCs from HFD-fed mice. n GSEA demonstrating the downregulated expression of VDR pathway genes in BMSCs from HFD-fed mice. N = 3, *P < 0.05, **P < 0.01, ***P < 0.001
