Fig. 7: H3K9me3 regulates the retrotransposon activity induced by critically short telomeres.
a ChIP-seq read density heatmaps for differentially enriched H3K9me3 peaks around the TSS (+/– 50 kb) and the corresponding H3K9me2 signal in WT and G4 Terc−/− ESCs. The relative density of H3K9me3 enrichment was presented in red, as indicated by the scale bar. The heatmap was generated using NGSPLOT. b H3K9me3 enrichment on telomeres. The number of reads was mapped to telomere (TTAGGG) repeats and normalized to the total number of reads in each sample. The number of reads was used to indicate H3K9me3 abundance at telomeres in two biological replicates. c The number of downregulated H3K9me3 peaks on retrotransposons, subtelomeres and subtelomeric retrotransposons in G4 Terc−/− ESCs. H3K9me3 peaks indicate their genome-wide enrichment, excluding telomere regions. d Metagene expression analyses of genes flanked by H3K9me3 peaks. For both the 5′ and 3′ genomic directions of H3K9me3 peaks, the median log2 fold changes of genes around peaks with decreasing (in red) or increasing H3K9me3 (in grey) in different window sizes are plotted. e L1MdGf as an example of expression and H3K9me3 change by short telomeres. f, g Coverage plot of ChIP-seq and RNA-seq reads on the consensus sequence of LINE1 family member L1MdTf (f) and L1MdGf (g). The y-axis indicates relative RPKM of sequencing reads. The x-axis indicates the full length of the corresponding retrotransposons.
