Extended Data Fig. 1: Creation and characterization of uninfected enhancer-deleted mice.

(a) Sanger sequencing trace of enhancer-deleted mice at site of enhancer deletion (bottom) with base-pair annotation (middle) compared to wildtype sequence (top) with regions of homology highlighted (red, blue boxes) as well as site of sgRNA binding noted (black boxes). (b) Gating strategy for baseline immune characterization, panel 1 (top row, T cell subsets) and panel 2 (bottom row), non-T cell lymphocytes. (c) Percentage of the indicated immune cell type of Live CD45⁺ cells in spleen (left) and liver (right) at baseline in EnhDel (n = 8) and WT (n = 6) mice. One of two representative experiments shown, significance calculated using an unpaired Student’s t-test. Errors bars represent mean and standard deviation. (d) Percentage of the indicated immune cell type expressing PD-1 in the spleen at baseline in EnhDel (n = 8) and WT (n = 6) mice. One of two representative experiments shown, significance calculated using an unpaired Student’s t-test. Errors bars represent mean and standard deviation. (e) Representative flow cytometry plot of PD-1 expression in CD8⁺ T cells and CD4⁺ Treg cells from EnhDel and WT mice. (f) Representative flow cytometry plots of CD25 (left), CX3CR1 (center), CD62L and CD44 (right) in CD8⁺ T cells from the spleen at baseline. (g) Chromatin accessibility tracks from ImmGen from immune populations in the spleen without stimulation. Enhancer of interest (−23.8 kb) highlighted in blue box. (h) Representative flow cytometry plots of Cell Trace Violet (CTV) following 72 hours of in vitro stimulation (left), and quantification of division number by CTV dilution (right) in EnhDel and WT cells. Dots represent individual mice; n = 8 mice for EnhDel, n = 6 mice for WT. One of two representative experiments shown, significance calculated using an unpaired Student’s t-test. Bar height represents mean, error bars represent standard deviation. Asterisks used to indicate significance correspond to the following: ns, not significant (P > 0.05), *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001 and ****P ≤ 0.0001.