Fig. 2

Comparison of MoDLE with OpenMM and Micro-C data. A Simulated MoDLE contact frequencies solely mediated by LEFs. B Intra-TAD contacts (only) generated with MoDLE. C Lower triangle: Loop extrusion and intra-TAD contacts from MoDLE in the same region as for A and B. Upper triangle: Micro-C data from the same region. D Side-by-side comparison of Micro-C data, MoDLE output, and OpenMM output for a region on chromosome 3 in H1-hESC. E Quantitative comparison of the accuracy (fraction of correctly classified pixels relative to all pixels) of MoDLE and OpenMM in reproducing stripe and dot pixel-patterns observed in modeled regions in H1-hESC cells (see the “Methods” section). F In silico simulated molecular contacts mimicking CTCF and WAPL depletion. Left: Wildtype (WT) output of MoDLE in a region on chromosome 6 in H1-hESC. Middle: effect on MoDLE output when CTCF barriers weakly associate with their binding sites. Right: effect on MoDLE output when LEFs are less likely to be released from DNA, thus mimicking WAPL depletion