Extended Data Fig. 6: Epigenetic program regulated by TOX.
From: TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion
a, Left, location of differentially accessible ATAC–seq peaks from Fig. 6a (top) or Fig. 6f (bottom). Right, distribution of all peaks in CD8+ T cells that are above background levels. b, c, ATAC–seq and RNA-seq tracks of Teff-cell-associated (b) or Tmem-cell-associated (c) loci. Peaks uniquely opened (b) or closed (c) in Tox−/− relative to wild-type T cells are highlighted with grey bars. d, Enumeration of significantly differentially accessible sites (FDR < 0.05) in wild-type and Tox−/− T cells at Tex-cell-specific and Teff-cell-specific loci13. e, PSEA of chromatin regions specifically accessible in naive T, Teff, Tmem cells13 in Tox−/− compared with wild-type P14 T cells. f, Fold change in ATAC accessibility versus RNA expression. Key genes for Tex and Teff cells are highlighted and genes associated with multiple peaks are connected with a red line. Inset, a table enumerating the number of gene–ATAC peak pairs in each quadrant. g, PSEA of chromatin regions specifically accessible in naive T, Teff, Tmem cells in TOXOE compared with control P14 T cells. h, ATAC–seq tracks of naive T, Teff, Tmem and Tex cells13 compared with control and TOXOE T cells at the Pdcd1 locus. The grey bar highlights the Tex-cell-specific −23.8-kb enhancer. i, Abundance, specificity and reproducibility plot of proteins identified by mass spectrometry after TOX immunoprecipitation compared with IgG control in EL4 cells. Hits are coloured using the MiST score (blue signifies >0.75). j, Gene ontology biological process enrichment of TOX-bound proteins identified in i with MiST score >0.75.
