Figure 1. CHART-seq reveals a two-step mechanism of Xist spreading during de novo XCI.
a, Xist RNA is enriched on Xi. Normalized read densities displayed in mus, cas, and composite (comp) tracks. b, Coverage of enriched segments on chrX and autosomes. c, Xist coverage at indicated timepoints relative to gene silencing. Enriched segments shown beneath in gray. Brackets, y-axis scale. Xist peaks at d0 have less amplitude and density, but reflect d3 and d7 patterns, and are Xi-enriched (Extended Data Fig. 2f), consistent with initial Xist spreading to local regions, suggesting initial differentiation in a subfraction of cells. RNAseq of d7 and MEF shown below. Skewed allelic expression consistent with Xi-silencing (value −0.5 = 3-fold expression difference between Xi and Xa). d-e, Xist CHART signals (40 kb bins) from d7 correlate with d3 (d) and MEF (e)(see Extended Data Fig. 3). Regions showing >10-fold differences after normalization are colored purple and displayed on the X (lower panels). f, Depletion of Xist at a representative escapee. g, Xist preferentially targets genes in active chromatin (H3K4me3-marked on d7). Xist densities shown for gene bodies of active (n=532), inactive (n=475), and escapee genes (n=10). Medians are indicated. Individual data points overlaid on boxplot; error bars, 1.5-fold interquartile range. *p<0.05, **p<1×10−8, ***p<2.2×10−16 , Mann-Whitney U tests. h, Xist RNA distribution from d7 cells relative to chromatin features.