Figure S3.
Gene repression upon IR is associated with the loss of H3K9me3 at intronic L1Md loci harboring NF-κB binding sites. (A and B) H3K9me3 enrichment in the NIR conditions evaluated by ChIP-qPCR at long (>5 kb) intronic L1Md promoters of the indicated genes compared to Spi1 (A and B), and at L1_A promoter compared to repetitive 5S ribosomal RNA (A). Results are expressed as the means ± SEM of the percentage of input. Each dot represents a pool of three mice from two to four independent experiments. (C) H3K9me3 ChIP-qPCR enrichment 1 mo after TBI. Each dot represents a pool of three (NIR) or four (IR) mice from two to three independent experiments. Results are means ± SEM of the percentage of input normalized to the NIR condition. t test. (D) Gating strategy for electroporated siglo+ HSCs in del L1Md condition using nonelectroporated cells as a control for designing FITC gate. (E) To test the efficiency of the different combinations of gRNAs, DNA amplification of Mecom L1Md was assessed and normalized to the amplification of Snx27 L1Md by qRT-PCR. In red, the couple of guides that were selected for further analysis. (F) DNA amplification assessed by qRT-PCR and in Cas9-gRNA RNP electroporated HSCs 48 h after irradiation in vitro. Ct values were normalized to L1-Snx27. t test. (G–L) De novo motif discovery analysis performed with the BaMMmotif tool on L1Md sequences located in: introns of downregulated genes vs. upderegulated genes (G); genes participating vs. not participating to the loss of the low-output or MK-biased HSC signatures (H and I); promoter sequences (−2 kb; +1 kb TSS) from downregulated vs. nonderegulated genes (J); L1Md located in genes from the HSC signature vs. genes from other organs signatures (kidney + liver + pancreas + testis + salivary gland + placenta) from Su et al. (2002) (K). (L) L1Md located in genes from the Gene Ontology (GO) term immune response process (GO:0002376) vs. genes from the GO term reproductive process (GO: 0022414). Enriched motifs were matched to known motifs using the Hocomoco mouse database. *, P < 0.05; ****, P < 0.0001.

Gene repression upon IR is associated with the loss of H3K9me3 at intronic L1Md loci harboring NF-κB binding sites. (A and B) H3K9me3 enrichment in the NIR conditions evaluated by ChIP-qPCR at long (>5 kb) intronic L1Md promoters of the indicated genes compared to Spi1 (A and B), and at L1_A promoter compared to repetitive 5S ribosomal RNA (A). Results are expressed as the means ± SEM of the percentage of input. Each dot represents a pool of three mice from two to four independent experiments. (C) H3K9me3 ChIP-qPCR enrichment 1 mo after TBI. Each dot represents a pool of three (NIR) or four (IR) mice from two to three independent experiments. Results are means ± SEM of the percentage of input normalized to the NIR condition. t test. (D) Gating strategy for electroporated siglo+ HSCs in del L1Md condition using nonelectroporated cells as a control for designing FITC gate. (E) To test the efficiency of the different combinations of gRNAs, DNA amplification of Mecom L1Md was assessed and normalized to the amplification of Snx27 L1Md by qRT-PCR. In red, the couple of guides that were selected for further analysis. (F) DNA amplification assessed by qRT-PCR and in Cas9-gRNA RNP electroporated HSCs 48 h after irradiation in vitro. Ct values were normalized to L1-Snx27. t test. (G–L) De novo motif discovery analysis performed with the BaMMmotif tool on L1Md sequences located in: introns of downregulated genes vs. upderegulated genes (G); genes participating vs. not participating to the loss of the low-output or MK-biased HSC signatures (H and I); promoter sequences (−2 kb; +1 kb TSS) from downregulated vs. nonderegulated genes (J); L1Md located in genes from the HSC signature vs. genes from other organs signatures (kidney + liver + pancreas + testis + salivary gland + placenta) from Su et al. (2002) (K). (L) L1Md located in genes from the Gene Ontology (GO) term immune response process (GO:0002376) vs. genes from the GO term reproductive process (GO: 0022414). Enriched motifs were matched to known motifs using the Hocomoco mouse database. *, P < 0.05; ****, P < 0.0001.

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