Figure 6. Increased TCR signaling drives thymic Treg cell differentiation in the absence of CNS0.

A-D. ATAC-seq of indicated populations sorted from the thymuses of 16-week-old CNS0^FL and CNS0^Δ male littermates. See STAR Methods for details.

A. Enrichment (presence in target versus in background) of known TF motifs, determined by HOMER, in summit-centered peaks of OCRs significantly more accessible in CNS0^Δ Treg cells. Top 20 are shown, all with q <0.05 and ranked by enrichment.

B. K-means clustering of OCRs with significant differential accessibility in any pairwise comparison. Columns show individual samples and data are normalized by Z-scores per row. Right-hand columns indicate proportion of OCRs significantly more accessible in CNS0^Δ Treg cells (left) or CNS0^FL Treg cells (right) within each cluster.

C. Enrichment (presence in target versus in background) of known TF motifs, determined by HOMER, in summit-centered peaks of OCRs in k-means cluster I. Top 20 are shown, all with q <0.05 and ranked by enrichment. Coloring indicates families of DNA-binding domains.

D. K-means clustering of OCRs with significant differential accessibility between CNS0^Δ and CNS0^FL Treg cells. Columns show individual samples and data are normalized by Z-scores per row.

E. Frequencies of Vβ5⁺ cells among indicated populations from the thymuses of 6- to 10-week-old CNS0^FL and CNS0^Δ male littermates. Each point indicates 1 mouse. Data are pooled from 2 experiments.

F-H. Inverse Simpson index indicating the diversity intensity (F, G) and total unique TCR clones (H, I) of TCRβ (F, H) or TCRα (G, I) chain sequences from splenic Treg cells isolated from 6-week-old CNS0^FL and CNS0^Δ male mice. Each point indicates 1 mouse and data are from a single experiment.

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

See also Figures S6 and S7.