Fig. 2: Senescence caused by loss of DNA methylation is accompanied by an interferon response and a SASP signature.

A Experimental scheme of sample collection for bulk RNA sequencing (RNA-seq), whole-genome bisulfite sequencing (WGBS) and single cell RNA sequencing (scRNA-seq). B Number of differentially expressed genes (DEGs) at the indicated days of Dox/Auxin treatment. DEGs were identified using DESeq2 tool. P values were calculated using a two-sided Wald test and adjusted for multiple comparisons via the Benjamini-Hochberg (BH) method. Up-regulated genes (red): adjusted p value < 0.05 and log2 FoldChange > 1. Down-regulated genes (blue): adjusted p value < 0.05 and log2 FoldChange < −1. Light gray dots: no significant change. C Venn diagram of significantly up-regulated DEGs. D Gene set enrichment analysis (GSEA) of selected gene sets from the Molecular Signatures Database (MSigDB). The heatmap represents the normalized enrichment score (NES) in each comparison at the indicated days. Significantly enriched gene sets are shown in red; significantly depleted gene sets are displayed in blue. Conditions with an asterisk are significant with a false discovery rate (FDR)  <  0.05. E Combined analysis of the WGBS and bulk RNA-seq data identifies genes for which loss of promoter DNA methylation correlates with gene activation. The promoter region is defined from −1200 bp to 300 bp relative to the transcription start site (TSS). Enrichment analysis was performed using clusterProfiler package. Significantly enriched terms were identified by a one-sided Fisher’s exact test. Enriched Hallmark pathways (MSigDB) for these genes are shown with dot plot indicating gene ratio and BH-adjusted FDR. F UMAP visualization of scRNA-seq data from degron cells at day 8 of treatment. Left: colored by sample; right: colored by clusters. G Analysis of the corresponding Leiden clusters. Top: bar plot showing the number and proportion of cells per cluster from each sample. Bottom: GSEA analysis of selected gene sets per cluster. Dot size represents significance (–log10 FDR), and color indicates scaled NES. Source data are provided as a Source Data file.