Frequency of nuclei transcribing both alleles of neighbouring loci.

Expected frequencies of nuclei transcribing from both allelels of neighbouring loci were calculated from observed frequencies of 2Z-active (or 2X-active) nuclei (Table S1 and S2). For example, SMARCA2 was 2Z-active in 76% of nuclei and PTPRD was 2Z-active in 60% of nuclei. Therefore, it was expected that they should both be 2Z-active in 0.76*0.6 (45.6%) of nuclei. P-values were calculated with a X2 test with 1 degree of freedom. Bonferroni correction was conducted.