Extended Data Fig. 1: Characterization of chromatin compartmentalization and TAD dynamics during transdifferentiation. | Nature Genetics

Extended Data Fig. 1: Characterization of chromatin compartmentalization and TAD dynamics during transdifferentiation.

From: CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response

Extended Data Fig. 1

a, Genome-wide Pearson correlation matrix between PC1 values of Hi-C samples at different time points. b, Scatter plots of PC1 values (n = 1,332 100-kb bins) showing changes relative to initial B cell genome compartmentalization for chromosome 12. c, Line chart depicting fractions of the genome assigned to A or B compartments at 10 time points during transdifferentiation. Y-axis represents the number of 100-kb bins. d, Gene ontology analysis of genes in regions switching from B to A (n = 980 genes) or A to B (n = 1,815 genes) compartments (P values, FDR corrected Fisher test). e, CTCF binding signal at TADs, normalized for TAD size in samples at various transdifferentiation time points. f, PCA of insulation score values at TAD borders during transdifferentiation (n = 4,006 TAD borders). Grey arrow depicts an averaged trajectory. g, RNA expression of genes at TAD borders gained (n = 254 genes) or lost (n = 293 genes) during transdifferentiation. All box plots depict the first and third quartiles as the lower and upper bounds of the box, with a thicker band inside the box showing the median value and whiskers representing 1.5x the interquartile range. h, Homer DNA motif analysis at ATAC-seq peaks detected at stable (n = 2,044), gained (n = 591) or lost (n = 135) TAD borders (P values are calculated using hyper-geometric statistical tests).

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