Extended Data Fig. 1: Expression of H3.3 chaperones in haematopoietic cells, creating Daxx F/F mice and analysis of LT-HSC ATAC-seq and RNA-seq data.
a, Heatmap of Daxx, Atrx and Hira expression levels (data from18). b, Daxx genomic locus, Daxx floxed locus following homologous recombination, conditional KO allele following deletion of the FRT-flanked or F3-flanked Neomycin (NeoR) and Puromycin (PuroR) resistance gene; Cre-mediated deletion of Daxx exons 2-7. c, PCA for ATAC-seq data (3 w.p.i.; top-500 most variable peaks): displayed principal components (PC) 1 versus 2. d, Enriched IPA immune system-related canonical pathways for ERV-overlapping enhancer peaks that open upon Daxx KO in LT-HSCs (3 w.p.i.). e, Enriched IPA immune system-related biofunctions for ERV-overlapping enhancer peaks that open upon Daxx KO in LT-HSCs (3 w.p.i.). f, PCA plot for LT-HSC RNA-seq data (3 d.p.i.). g, Counts per million of LINE and SINE elements in LT-HSCs (3 d.p.i.). h, Genome browser tracks of the regulatory region of Spi1, Mki67 and Egr1 (3 d.p.i.). i, ATAC-seq coverage around TERRA-BS across all chromosomes or across sex chromosomes at 3 w.p.i. and 3 d.p.i. j, Genome browser tracks for wild-type (blue) and Daxx KO (red) LT-HSCs (ATAC-seq: 3 w.p.i. and 3 d.p.i.; RNA-seq: 3 d.p.i.) around Erdr1, Mid1, Gm1976 and Wls; TERRA CHIRT-seq based on published data23. Light-blue regions are called TERRA binding sites and yellow region highlights the Gm1976 gene. For Gm1976 and Wls boxes show ATAC-seq coverage at the major TERRA binding site. LT.HSC, long-term haematopoietic stem cells; ST.HSC, short-term haematopoietic stem cells; MPP, multipotent progenitor; CMP, common myeloid progenitor; GMP, granulocyte-monocyte progenitor; CLP, common lymphoid progenitor; MEP, megakaryocyte erythroid progenitor. n = 2 independent biological samples analysed 3 weeks post induction with tamoxifen (c−e, i, j). Analysis of gene expression and chromatin accessibility of LT-HSCs from n = 2 Daxx + /+ and Daxx + /F as well as n = 3 Daxx F/F samples collected 3 days post final induction with tamoxifen (f-j). Data are Activation Z-score from IPA Fisher’s exact tests with multiple testing adjusted p-values < 0.05 (d, e). Activation Z-score > 2 suggests increased activation of shown biofunctions. Numerical source data provided in Source data.
