Extended Data Fig. 3: Shared features of CAR-dependent gene expression in mucosal T cells and hepatocytes.
From: CAR directs T cell adaptation to bile acids in the small intestine
a, Overlap between genes induced in B6 wild-type mouse hepatocytes by in vivo treatment with TC or PCN, relative to vehicle (CO, corn oil). b, Enrichment of genes induced by TC, but not PCN, in mouse hepatocytes (as in a), within those reduced in CAR-deficient (B6.Nr1i3−/−) versus wild-type (B6) siLP Teff cells from week-3 congenically co-transferred Rag1−/− mice (as in Fig. 2a–c). Nominal P values compare observed NESs to the null distribution for 1,000 permutations. c, Differential gene expression, determined by DESeq2 and shown as a volcano plot, between CAR-deficient (B6.Nr1i3−/−) and wild-type (B6) siLP Teff cells re-isolated from transferred B6.Rag1−/− mice, as in Fig. 2a. Genes induced by TC, but not PCN, treatment in mouse hepatocytes (as in a; purple), bound by CAR in ChIP–seq analysis of hepatocytes from TC-treated mice (blue), or both (red) are highlighted. Chi-square P values are indicated. d, CAR occupancy, determined by ChIP–seq, at representative loci whose expression is regulated by CAR in both mucosal T cells and hepatocytes within mouse hepatocytes ectopically expressing epitope-tagged mouse (m) or human (h) CAR proteins and re-isolated from mice after treatment with TC or CITCO. *False discovery rate (FDR) q < 0.05 determined using MACS2 base settings.
