Fig. 2

Highly variant TAD-like single-cell domains are present on both inactive and active X chromosomes in IMR-90 cells (target region as stated in Fig. 1). A Examples of individual spatial distance matrices from single copies of inactive X chromosomes. B Examples of individual spatial distance matrices from single copies of active X chromosomes. Gray rows and columns in A and B indicate undetected loci. The yellow lines in A and B represent the ensemble TAD boundary. C The boundary probabilities of single-cell domains in inactive X chromosomes. D The boundary probabilities of single-cell domains in active X chromosomes. Note the higher boundary probability at the population averaged TAD boundary (arrow). The horizontal lines in C and D represent the mean probabilities (orange) and plus/minus one standard deviation (blue). CTCF and RAD21-binding peaks are illustrated in blue and red respectively. E The boundary strengths of single-cell domains in inactive X chromosomes. F The boundary strengths of single-cell domains in active X chromosomes. G Cooperativity of chromatin interaction in inactive and active X chromosomes. For all ordered triplets in the traced chromatin region, contact probabilities (defined with 200-nm proximity threshold) of genomic loci B and C given contact/non-contact of genomic loci A and B are shown in red and blue, respectively. “Ordered” means that the locus numbers of A, B, and C are in an ascending order. The unconditional contact probabilities between loci B and C are shown in black. The triplet indices are arranged in an ascending order based on the unconditional contact probabilities between loci B and C. N = 483 for C, E, and the left panel of G. N = 477 for D, F, and the right panel of G