Supplementary Figure 8: ChIP-Seq analysis of TCF-1 in CD8⁺ T cells.

(a) Numbers of TCF-1 peaks identified using stringent and permissive settings of the MACS algorithm. Under the stringent setting, 2,827 peaks were defined as stringent TCF-1 peaks, and under the permissive settings, 6,577 additional peaks were defined as permissive TCF-1 peaks. (b) Genomic distribution of all TCF-1 binding peaks. Promoter region is defined as “-5 kb to +1 kb” flanking the transcription start sites of known RefSeq genes. (c) Overlap of TCF-1 binding peaks with H3K4me3 and H3K27me3 peaks in human naïve CD8⁺ T cells. The homologous regions of the H3K4me3 and H3K27me3 peaks from human CD8⁺ T cells were identified in mouse genome using the LiftOver tool. TCF-1 binding peaks in different genomic regions were then assessed for peak overlapping. The criterion for overlapping is that the closest boundary-to-boundary distance of two peaks is within 400 bp. (d) TCF-LEF and (e) Runx motifs found in the permissive TCF-1 binding peaks. The motif logos are shown. Note that the motifs found in the permissive TCF-1 peaks are consistent with those found in the stringent TCF-1 peaks (Fig. 8c and 8d). (f) Venn diagram showing the motif distribution in the permissive TCF-1 peaks.