Extended Data Fig. 6: Gene and TE expression in Setdb1 KO LLC and B16 cells.

a, Distribution of TE types (top) and LTR subfamilies (bottom) induced in Setdb1 KO LLC or B16 cells by RNA-seq. b, Heat map showing RNA expression (row normalized) of canonical interferon-stimulated genes in untreated and poly(I:C) stimulated (500 ng ml⁻¹, 48 h) control and Setdb1 KO LLC and B16 cells. c, Percentage of TEs induced in Setdb1 KO LLC or B16 cells that retain intact viral ORFs, compared to control TEs. Statistics by Fisher’s exact test. d, Flow cytometry for cell-surface expression of the MuLV envelope protein in Setdb1 KO LLC and B16 cells. Gating strategy (left) and histograms (right) with mode-normalized cell counts are shown. Data are representative of n = 3 and n = 2 experiments in LLC and B16, respectively. e, Differential protein expression in B16 cells by whole-cell mass spectrometry. Tryptic protein sequences derived from TEs (red) or canonical proteins (grey) are highlighted. Fold-change (x-axis) and statistical significance (y-axis) for proteins in Setdb1 KO versus control are shown. f, Venn diagrams showing the number of predicted, unique TE-encoded H2-K^b/H2-D^b binding peptides in LLC and B16 cells by GRCm38 RNA-seq analysis. Diagrams show the total number of predicted, TE-encoded MHC Class I peptides in LLC and B16 cells (left), and subsets showing (1) high expression in control cells and further induction upon Setdb1 KO (middle), and (2) no detectable expression in control cells and strong induction only upon Setdb1 KO (right). Several MuLV-encoded peptides known to be presented by H2-K^b or H2-D^b are highlighted. ***P < 0.001. ****P < 0.0001.