Fig. 5
Trajectory analyses based on allelic CDPs reveal distinct conformational states during differentiation. A Semi-supervised genome-wide trajectory analysis of F121 cells based on allelic CDPs (see Fig. 2 I and the “Methods” section) from sci-Hi-C data using Monocle2 DDRTree. Allelic CDPs for each chromosome were concatenated together for each of 2056 F121 cells with at least 100 contacts per chr1 and chrX allele. 2040 significantly differential bins from the genome-scale concatenated allelic CDPs across time points with q-value ≤ 10−11 were used to construct the trajectory. Each data point represents a cell colored by time point. Arrows indicate the direction of development in pseudotime. Branches are labeled according to developmental state: branch 1 is the root embryonic stem cell (early) branch; branch 2 captures an intermediate state (intermediate branch); and branch 3 captures the genome architecture of differentiated cells including NPCs (differentiated branch). Inset table gives cell counts per time point per trajectory branch as well as the time point color used for data points in the plot. See also Additional file Fig. S5A–E. B As in A, but based on 1924 significantly differential bins (q-value ≤ 10−11) for autosomal allelic CDPs. C As in A, but based on 178 significantly differential bins (q-value ≤ 10−5) for chrX CDPs. Three early sub-branches were considered to be a single early branch (Additional file 1: Fig. S5C). D As in A, but with cells colored by pseudotime with respect to the root ESC branch. E As in A, but highlighting the most distal cells on each branch of the trajectory. The inset table gives the proportion of cells classified as distal and non-distal. Pseudotimes for each branch were renormalized to fall between 0 and 1 and the following thresholds were used to classify cells as distal for the early, intermediate, and differentiated branches respectively: 0.91, 0.83, and 0.73 (see F). F Cumulative distributions (CDFs) of the proportion of cells along each branch of the trajectory in A. Vertical dashed lines show the inflection points in the plots chosen for determining the threshold for calling distal cells in E. G Allelic CDPs for chr1 (left column) and chrX (right column) (129 in red, cast in blue) for cells at the distal ends of the three branches (rows) from the trajectory described in E. For binning and scaling details of the plots as described in Fig. 3A. H Plots of the log2 ratios between allelic CDPs for cells at the distal ends of each pair of branches (rows) in the trajectory described in E for every logarithmic bin (2^x where x was incremented by 0.125) for the 129 (red) and cast (blue) alleles of chr1 and chrX. Top row: intermediate vs. early branch. Middle row: differentiated vs early branch. Bottom row: differentiated vs. intermediate branch. The dashed line reflects no difference between the two groups of cells and yellow highlighting reflects bins that show a significant difference (adjusted p-value <10−6) between the two groups of cells (Additional file 1: Fig. S5F)