Fig. 1: Transcriptome of differentially expressed genes and retrotransposons of various cell types from Terc^−/− and WT mice.

a Overall experimental design. Several types of cultured cells and tissues from WT and G3 Terc^−/− mice were used for multi-omics analysis, including the transcriptome analysis by RNA-seq, whole-exome sequencing (WES), third-generation whole-genome sequencing, and epigenome analysis using ATAC-seq, ChIP-seq of H3K9me3, and Hi-C sequencing. b Heatmap showing the correlation of the expressed genes among the cell types and tissues. ESC embryonic stem cell (P18 for early passage and P42 for late passage), TTF tail-tip fibroblast, ASC adipose-derived mesenchymal cell. The passage number for somatic tissues is P3. The bar color represents the correlation coefficient of the samples. c Volcano plot of differentially expressed genes (DEGs) in Terc^−/− and WT cells of various cell types. Red dots, upregulated genes with fold change > 2 and P value < 0.05; blue dots, downregulated genes with fold change > 2 and P value < 0.05; grey dots, genes without significant change. Early-passage G4 Terc^−/− ESC (P18), late-passage G4 Terc^−/− ESC (P42), G3 Terc^−/− TTF (P3), G3 Terc^−/− ASC (P3), and fresh tissues were collected. d MA plot illustrating differentially expressed retrotransposons of the LINE1, ERV1, ERVL and ERVK classes in Terc^−/− and WT cells or tissues. Significantly changed retrotransposons are shown in different colors according to class. e Heatmap of all differentially expressed TEs by fold change in short telomere tissues or cells compared with WT tissues or cells. The bar color represents the fold change of the expression of TEs in Terc^−/− vs WT cells; red indicates retrotransposons upregulated in Terc^−/− vs WT cells; blue indicates retrotransposons downregulated in Terc^−/− vs WT cells.