Hi-C dot strength versus distance requires dynamic boundaries. (A) Convergent dot scores as a function of genomic distance were calculated between pairs of convergent barriers from contact maps binned to 10-kb resolution. First, genomic distances were binned into 25 logarithmically spaced bins between 100 and 5000 kb (dashed lines overlaid on map). Second, 80-kb snippets centered on barrier pairs in each genomic distance range were collected and averaged (snippet centers shown as dots overlaid on map, averaging shown below). Dots scores at each genomic distance were computed as the ratio of contacts in the snippet center relative to four control regions (right). (B) Convergent dot scores as a function of genomic distance for experimental control (blue) and WAPL depletion data sets (yellow), both from Liu et al. (2021). (C) Convergent dot scores as a function of genomic distance for simulations. Plots show extruders with either reference (blue) and higher (orange) lifetimes at three CTCF bound times (i: 150 sec, ii: 600 sec, iii: 1500 sec, iv: 9000 sec). Only simulations with τb < τE displayed similar behavior to experiments (ii), where the higher-lifetime curve starts lower and has a peak after the wild-type curve. (D) Heat map of simulated distance-averaged dot scores for convergent pairs of barriers over all distances. Note higher scores for larger τb at fixed occupancies. Dashed lines indicate experimental dot scores for mESCs from Bonev et al. (2017) or control from Liu et al. (2021), and i–iii indicate dot scores computed from curves in C. Note that τb in iv exceeds the displayed range in the heat map. (E) Distance-averaged convergent dot score for extruders with reference or higher lifetimes, indicating stronger dots for the latter, particularly at higher τb. (F) Distance-averaged convergent dot scores for experimental and simulated data. Experimental dot scores from Liu et al. (2021) increased after WAPL depletion. Simulations for indicated τb shown for either reference (blue) or increased (yellow) lifetime.
