Figure 5. Increased cell-intrinsic activation partially compensates for CNS0-deficiency.

A. Schematic of the generation of bone marrow chimeric (BMC) mice analyzed in (B, S5A-C). See STAR Methods for details.

B. Frequencies of Foxp3-GFP⁺ Treg cells among CD45.2⁺CD4⁺ T cells in indicated tissues (LN: pooled brachial, axillary, and inguinal lymph nodes; LPL: small intestine lamina propria; PP: Peyer’s patches) of CNS0^FL or CNS0^Δ BMC mice. Blue symbols indicate ratios of CNS0^Δ to CNS0^FL Treg cell frequencies. Each point indicates 1 mouse, and data are representative of 2 independent experiments.

D, E. RNA-seq of CNS0^Δ versus CNS0^FL Treg cells sorted from the thymuses of 8-week-old CNS0^Δ/WT and CNS0^FL/WT female littermates.

Cumulative distribution function plot of gene expression (log₂ fold change, FC). All genes (black) and genes with increased (red) or decreased (blue) expresison in activated vs. resting Treg cells. p, one-tailed Kolmogorov-Smirnov test.

E. Heatmap showing row Z-score normalized gene expression. Genes are restricted to those contained in the indicated gene sets (activated vs resting Treg) and significantly differentially expressed (adjusted p-value <0.05) between genotypes.

F, G. RNA-seq of Treg cells sorted from the thymuses of 8-week-old CNS0^FL and CNS0^Δ male littermates.

F. Cumulative distribution function plot of differentially expressed genes (log₂ FC). All genes (black) and genes with increased (red) or decreased (blue) expresison in TCR-bearing vs. TCR-deleted Treg cells. p, one-tailed Kolmogorov-Smirnov test.

G. Heatmap showing row Z-score normalized gene expression. Genes are restricted to those contained in the indicated gene sets (TCR-dependent genes) and significantly differentially expressed (adjusted p-value <0.05) between genotypes.

(B) Unpaired t-tests with correction for multiple comparisons using the Holm-Sidak method. p >0.05 ns, <0.01 **, <0.001 ***, <0.0001 ****.

(D, F) p, by one-tailed Kolmogorov-Smirnov test.

See also Figure S5.