Fig. 6

Epiphany predicts TAD boundary changes due to epigenomic perturbations. A Mouse ES E12.5 Capture Hi-C data from Despang et al. [28] for WT (top), 4 CTCF sites depletion (middle), and the absolute difference between the two conditions (bottom). Data are publicly available at (GSE78109, GSE125294). Four CTCF sites depleted in the middle figure were at region (C1 site(mm9 chr11:111,384,818–111,385,832), C2-C4 site (chr11:111,393,908–111,399,229), marked with black dashed lines). Data are mapped relative to mm9. B Epiphany cross-species prediction of structural changes caused by CTCF perturbation. Epiphany was trained using human cell line GM12878, and predicted using mouse limb bud epigenomic data mapped relative to the mm10 assembly. The panel shows Epiphany prediction of WT mES Hi-C map with HiC-DC+ obs/exp ratio normalization (top row), the prediction of TAD fusion after masking CTCF sites at (mm10 chr11:111,520,000–111,540,000) (middle row), and the absolute difference between the two predictions (bottom row). Epigenomic tracks at the bottom are showing feature attribution (SHAP value) for highlighted vertical vector in the Hi-C contact map. The upper two tracks are the original CTCF track and corresponding SHAP values. The lower two tracks are CTCF tracks with peaks in the vertical line deleted and the corresponding SHAP values. C Capture Hi-C maps from Wu et al. [31] experimented at the Sox17 locus before (top) and after (bottom) targeting the CTCF sites. Data are publicly available at (GSE127196). Data are mapped relative to hg19. D Epiphany cross-cell type prediction of structural changed caused by CTCF deletion. CTCF sites at hg38 (chr8:54,165,000–54,170,000, in the vertical lines) near Sox17 locus is deleted. Top row shows the Epiphany predicted Hi-C contact map before perturbation, and bottom row shows the predicted map after deletion. Vertical dashed line shows the location of the deleted CTCF site