Supplementary Figure 6: ChIP-Seq analysis of the binding of TCF-1 to the Thpok and Cd4 loci

ChIP-Seq of TCF-1 in whole thymocytes was reported by Li L et al. (Blood 122, 902, 2013), and ChIP-Seq of Runx3 in CD8⁺ T cells was reported by Lotem J et al (PLoS One, 8, e80467, 2013). The data were downloaded and processed for peak calling using MACS. Using the same stringent criteria (detailed in Supplementary Fig. 8), wherein 2,827 TCF-1 binding peaks were identified in CD8⁺ T cells, we found 32,663 peaks in whole thymocytes. Possible reasons for the higher numbers of TCF-1 binding peaks in whole thymocytes include: 1) TCF-1 may regulate different target genes during thymocyte maturation stages. The binding events detected in whole thymocytes are a collection of all TCF-1 binding events at different stages; and 2) the ChIP-Seq control sample was from input DNA for peak calling, whereas ChIP-Seq of TCF-1 and Runx3 by us and Lotem J et al used IgG or non-immune serum-immunoprecipitated samples as control. The ChIP-Seq track wiggle files were uploaded to the UCSC genome browser for visualization of enriched binding by the transcription factors. For the select gene locus, the transcription start site (TSS) and orientation are marked by arrows. The horizontal bars over TCF-1 or Runx3 tracks indicate the enriched binding peaks identified by MACS. (a) shows enriched binding of TCF-1 at the Thpok GTE in whole thymocytes but not in CD8⁺ T cells. (b) shows co-occupancy of TCF-1 and Runx3 at the Cd4 silencer in all cell types. TCF-1 is also associated with Cd4 enhancer and weakly with Cd4 promoter in whole thymocytes, consistent with reported TCF-1 binding to these regions by Huang Z et al (J. Immunol. 176, 4880, 2006). Note that no TCF-1 binding to Cd4 enhancer and promoter in CD8⁺ T cells.