H3K9me3 is mainly enriched at recent L1Md subfamilies in HSCs. (A) Experimental and bioinformatic analysis design for H3K9me3 ChIP-seq. Mice were subjected to 2 Gy total body irradiation (IR) or left untreated (NIR). Analysis was done on both U- and M-MRA. (B) Gating strategy for HSCs (LSK CD34⁻Flk2⁻) sorting. (C) Number of peaks with IDR score <0.05 in U- and M-MRA and in NIR and IR conditions. ***, P < 0.001; **, P < 0.01, t test. (D) Repartition of confident peak annotations in each genomic feature using annotateR in NIR conditions for U- and M-MRA. (E) Left columns: Heatmap of H3K9me3 enrichment at M-MRA confident peaks in NIR and IR conditions. Each row represents one-scaled H3K9me3 peak with ±4 kb flanking regions. The color scale represents H3K9me3 enrichment over the input (H3K9me3 concentration) with the red corresponding to lower enrichment, and the blue to stronger enrichment. Center and right columns: Genomic coverage of the H3K9me3 peaks showed in the heatmap at different TE families and subfamilies (LINE, LTR, SINE, DNA, L1Md, Lx5) are also represented. Blue, TE is present; yellow, TE is absent in the peak (row).