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. Author manuscript; available in PMC: 2019 Jun 19.
Published in final edited form as: Immunity. 2018 Jun 19;48(6):1119–1134.e7. doi: 10.1016/j.immuni.2018.04.024

Figure 7. Satb1 and Runx1 roles in PU.1-mediated gene regulation in primary DN cells.

Figure 7

(A), Flow cytometric analysis of primary pro-T cells after CRISPR-Cas9-mediated knockout of PU.1, Satb1 or Runx1. (Upper) Experimental scheme. (Lower) sgRNA transduced BM-derived precursors after 8 days of OP9-DL1 culture. Representative of three independent experiments.

(B), Effects of Satb1 and Runx1 disruption on PU.1-mediated gene regulation in DN cells, by RNA-seq of transduced CD25+ DN cells from (A). Hierarchical clustering of expression changes in response to different treatments are shown, among genes down-regulated (top) and up- regulated (bottom) in PU.1-deficient DN cells (|Log2FC|>0.5, FDR<0.05, RPKM>1 in sgControl). Based on RNA-seq from independent duplicates.

(C), The binding patterns of PU.1 (DN1) and Runx1 (DN1 and DN3), and RNA-seq tracks are shown for Spi1 (PU.1), Satb1 and Runx1-deficient DN cells at the Itgax and Cd33 PU.1- dependent loci and at the Ly6d and Cd247 PU.1-repressed loci. Representative of two independent experiments. See also Fig. S6 and Table S5