3C-PCR was performed using the selected Xi primer pairs shown in ( A ) to detect potential chromatin contacts between P4 and P1. PCR products show the presence of chromatin contacts in WT and Xi-Inv, but not in Xi-Del1, which was used to exclude the possibility of any PCR products from contacts with P4 on the sp -Xa. Two biological replicates of 3C per genotype were performed except for WT with one additional replicate. Note that PCR products from chromatin contacts can vary in size, due to ligation of different DpnII sites from incomplete digestion, as predicted below the gels and in ( D ). PCR using genomic DNA (gDNA) from WT, Xi-Del1 and Xi-Inv1 shows no products from these B6-specific primer pairs, indicating the specificity of 3C-PCR.
