Fig 2: EOMES and RUNX3 interact within chromatin-associated complexes. a Selected EOMES-interacting proteins identified by RIME in activated CD8+ T cells. Total spectral counts for each replicate (anti-EOMES or control IgG) are shown. b Genomic distribution of EOMES (4306) and RUNX3 (6741)-binding sites in innate memory (TIM) cells. c Venn diagram illustrating the intersection between EOMES (in TIM) and RUNX3 (in naïve [N] and TIM cells) peaks at active promoters and enhancers. Density plots centered on common EOMES/RUNX3 or EOMES-specific peaks (±250 bp) represent the distribution of the best predicted sites of the JASPAR RUNX3 (MA0684.1) and EOMES (MA0800.1) motifs. d Representative EOMES, RUNX3, H3K4me1, H3K27Ac ChIP-seq, and ATAC-seq tracks at the Ly6c2 locus showing the co-localisation of EOMES and RUNX3 highlighted in grey (top). Sequence of the highlighted region and the location of EOMES and RUNX motifs with their position P-value are indicated (down). e Cumulative distribution plot generated by BETA algorithm showing the predicted activating/repressive functions of RUNX3 and EOMES with the indicated P-values determined by the Kolmogorov–Smirnov test. f Heatmap showing expression of genes from e that are predicted to be targets of EOMES. Selected genes are shown in the right margin. g Normalized coverage plot of histones modifications (H3K4me1, H3K4me3, and H3K27ac) and chromatin accessibility (ATAC-seq) centered on EOMES-binding sites at promoters and enhancers annotated to predicted genes from e. ChIP-seq was performed on three independent IPs (n = 7 mice per sample)

Fig 3: TIM cells display classical features of conventional memory cells. a Flow cytometry of CD3+CD8SP thymocytes from wild-type (WT) Balb/c mice. Histograms represent the expression of the indicated protein in EOMEShi (red) and EOMESlo (gray) cells or the fluorescence minus one (FMO) controls (empty). Median fluorescence intensity (MFI) or the proportion of positive cells are displayed. b SPADE of flow cytometry data gated on CD3+CD8SP thymocytes from WT Balb/c mice. Circles represent cell nodes, colors indicate expression levels for the indicated marker and size is related to the number of cells within a node. Annotations indicate the identified innate memory (TIM) subsets and the bulk of naïve cells. Trees displaying expression levels of other markers are shown in Supplementary Fig. 1. c SPADE trees showing cell frequency of CD3+CD8SP thymocytes from the indicated strain (b, c, 4 WT Balb/c mice were used for tree construction. In c, one representative mouse out of four is shown for each group). d SPADE trees showing cell frequency in each node for naïve and TIM cells sorted from WT Balb/c mice (gating, Supplementary Fig. 2). EOMES expression (horizontal bars indicate median ± interquartile range) in sorted naïve and TIM cells are shown. Each point represents an individual sample. Statistics were calculated using Mann–Whitney test. *P < 0.05. e Volcano plot of RNA-seq data from naïve versus TIM cells shows the adjusted P-value (–log10) versus fold change (log2) (up in TIM, red; up in naïve, green). The numbers of differentially expressed genes are indicated. RNA-seq was performed in triplicates (each sample was generated from a pool of at least seven mice). f BubbleGUM gene set enrichment analysis (GSEA) map of datasets from naïve (N), conventional effector (TE), and memory (TM) cells or from naïve and TIM CD8SP thymocytes. Gene sets (with the indicated number of genes) were established by analysis of their expression patterns between N, TE, and TM, from available gene sets or from naïve and TIM-specific genes as defined in e. The panel summarizes the normalized enrichment score (NES) and false discovery rate (FDR) parameters

Fig 4: SHH Regulates the Production of OB Interneurons and Oligodendrocytes in the Cortical SVZ Predominately by Reducing GLI3(A–D) Immunostainings for GSX2, SP8, EOMES, and OLIG2 in wild-type (control) (A), Smo cko (B), Gli3 cko (C), and Smo Gli3 dcko (D) mice at P0.(E) Quantification for the numbers of GSX2+, SP8+, EOMES+, and OLIG2+ cells per 300 mm width in the cortical VZ-SVZ of control and mutant mice at P0. Data are presented as means ± SEM; n = 3 mice per genotype. *p < 0.05; unpaired Student’s t test in (E). Scale bars, 200 mm in (D).

Fig 5: bMIPCs are mainly located in the human cortical IFL. A, B The cortical ISVZ contains many EOMES+ PYN-IPCs and a large number of migrating CGE-derived cortical interneurons (GABA+NR2F2+SP8+) at GW18. C Cortical bMIPCs (EGFR+ASCL1+OLIG2+, arrows) were mainly in the IFL. Note a large number of ASCL1+ PyN-IPCs (also EOMES+, see Fig. S11) in the cortical ISVZ, IFL and OSVZ. D Schema showing that human cortical CXCL12+ tRGs are in the VZ, a large number of CXCR4+ migrating cortical interneurons (CIN) and tRG-derived PyN-IPCs are in the ISVZ, resulting in the distribution of tRG-derived bMIPCs mainly in the IFL.