Supplementary Figure 3: Proof-of-principle experiment demonstrating the DLO Hi-C method.

a, K562 cells were double cross-linked with EGS and formaldehyde, digested with or without HindIII, and subjected to electrophoresis. b, The digested chromatin was ligated with or without the half-linkers by simultaneous digestion and ligation using T7 DNA ligase and HindIII and subjected to electrophoresis. c, Excessive linkers were removed by centrifugation. The linker-ligated chromatin complexes were precipitated after centrifugation, while the excessive MmeI linkers remained in the supernatant. d, Linker-ligated chromatin complexes were proximity ligated in gel by T4 DNA ligase, with the unligated sample (left lane) serving as a control. e, The proximity-ligated DNA was digested by MmeI to release the 80-bp DLO Hi-C DNA fragments, as indicated in the native PAGE image. f, Electrophoresis of the DLO Hi-C sequencing library. The experiment has been repeated three times independently with similar results.