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. 2024 Nov 15;221(12):e20240959. doi: 10.1084/jem.20240959

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© 2024 Li et al.

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Figure 6. — MCRS1 and YY1 coordinately regulate chromatin accessibility and immune sensitivity. (A) Metaplot and heatmap showing ATAC-seq signals around the TSS in control, Mcrs1^OX, and Mcrs1^OX;sgYy1 cells (n = 2 for both groups). (B) ATAC-seq profiles of genes that were bound by MCRS1 and differentially expressed in Mcrs1^OX cells. Genes were clustered based on ATAC-seq profiles, with the mean ATAC signals for each cluster shown on the right. (C) Chromatin accessibility at the MHC-I loci determined by ATAC-seq, with the upper panel showing tracks of ATAC-seq signals and the lower panel showing quantification of peaks around the TSS or distal non-coding regions (n = 2 for both groups; presented as means ± SEM; *, P < 0.05; **, P < 0.01; ****, P < 0.0001; MAnorm test). (D) MCRS1-regulated genes identified by differential expression in Mcrs1^OX cell and tumor (RNA-seq), direct binding by MCRS1 (ChIP-seq), and MCRS1/YY1-dependent chromatin accessibility change (ATAC-seq). A total of 39 genes met all these criteria, including the MHC-I genes. (E) The growth curves of control, Mcrs1^OX, and Mcrs1^OX;sgYy1 tumors in WT mice (n = 8, 8, 7 for control, Mcrs1^OX, and Mcrs1^OX;sgYy1, respectively; presented as Means ± SEM; ns, not significant, P ≥ 0.05; *, P < 0.05; two-way ANOVA with Tukey’s multiple comparisons test; N = 3 independent experiments). Illustration was created with https://BioRender.com. (F) Spider plots showing tumor volume changes in individual mice tumors as in E. (G) Tumor weights at the point of sacrifice (n = 8, 8, 7 for control, Mcrs1^OX, and Mcrs1^OX;sgYy1, respectively; presented as means ± SEM; ns, not significant, P ≥ 0.05; **, P < 0.01; ****, P < 0.0001; one-way ANOVA with Tukey’s multiple comparisons test; N = 3 independent experiments). (H) Analysis of CD8⁺ T cells in control, Mcrs1^OX, and Mcrs1^OX;sgYy1 tumors, analyzed by immunofluorescent staining (upper panel) and flow cytometry (lower panel) (n = 8, 8, 7 for control, Mcrs1^OX, and Mcrs1^OX;sgYy1, respectively; presented as means ± SEM; ns, not significant, P ≥ 0.05; *, P < 0.05; **, P < 0.01; ****, P < 0.0001; one-way ANOVA with Tukey’s multiple comparisons test; N = 3 independent experiments). Scale bar = 50 μm.