Fig. 8

Allelic expression and accessibility distributions show the onset of XCI-induced gene silencing. A Semi-supervised genome-wide trajectory analysis based on allelic expression data from sci-RNA-seq in female F121 cells with Monocle2 DDRTree using 4230 differentially expressed alleles across time points (q-value ≤ 0.01) and expression in at least 10 cells with a minimum total allelic expression of 160 UMI. Arrows indicate the direction of development in pseudotime. Branches are labeled according to developmental state: ESC branch, EB branch, and NPC branch. Tables below trajectories give cell counts and percentages per time point per trajectory branch as well as the time point color used for data points in the plot. B As in A, but based on allelic accessibility data from sci-ATAC-seq in female F121 cells for 17,455 of the top 50% most variable regions across the genome showing coverage in at least 10 cells and significantly differential across time points (q-value ≤ 0.01). C Distributions of differential expression from sci-RNA-seq between each homolog (log2 ratio of total 129 and cast expression) in female F121 cells at each time point (columns) for chr1 (top row) and chrX (bottom row) using genes expressed in at least 5 cells per group and cells with a total expression of at least 10 UMIs of expression from both alleles per chromosome. A 10% false-positive rate (FPR) threshold (absolute log2 ratio ≥ 1.2) based on the chr1 distributions was used to classify cells that had undergone XCI based on the log2 ratios of their total allelic expression. Cells with either their 129 or cast allele having undergone XCI would have an allelic ratio skewed to the left and right, respectively, as indicated on the d0 plot. The percentage of cells exhibiting 129 or cast XCI at each time point is shown at the top left and right, respectively, of each chrX distribution. See Additional file 1: Table S2. D As in C, but based on allelic chromatin accessibility data from sci-ATAC-seq. E Plots of the proportion (%) of F121 cells with a silenced chrX (light orange line) as determined by sci-RNA-seq, with a chrX with low accessibility (yellow line) as determined by sci-ATAC-seq, and with an Xi bipartite structure (blue line) as determined by sci-Hi-C (see C, D; Fig. 4D, E; Additional file 1: Fig. S7K–N)