Gene repression upon IR is associated with intronic L1Md. (A–C) Enrichment plots in IR vs. NIR conditions obtained from GSEA for TNF signatures induced in HSCs after TNF-α treatment 3 h in vivo and 3 and 12 h in vitro (A); MK-biased and serial engraftment HSC signatures (B); high output and multilineage differentiation signatures (C). (D) Quantitative analysis of H3K9me3 enrichment at promoters (−2 kb;+1 kb TSS) performed by U-MRA. Nonsignificant (blue dots) and significant (P < 0.05, pink dots) differential H3K9me3 enrichment at genes promoters are shown. (E) Correlation plot between H3K9me3 concentration at gene promoters vs. gene expression at genes presenting both significant deregulation and differential H3K9me3 enrichment at their promoters upon IR (P < 0.05). (F) Repartition of intragenic L1Md localization in the genes. TTS, transcriptional termination site. (G and H) Heatmaps of the expression of genes from MK-biased (G) and the low-output (H) HSC signatures that are significantly either upregulated (red) or downregulated (blue) in IR vs. NIR. Green stars indicate the presence of an intronic L1Md in the downregulated genes. FC, fold change; FDR, false discovery rate; NES, normalized enrichment score.