title: pnet2_abc_HiC
design: The Hi-C libraries and sequencing of rice samples were performed following the same protocol as described in earlier studies31,73. Briefly, the collected seedlings were cut into pieces and cross-linked with 2% formaldehyde solution for 15 minutes at room temperature in fume hood. Then, 2.5 M glycine was added to quench the cross-linking reaction. After nuclei extraction as described31, the chromatin was digested with a 4-cutter restriction enzyme MboI (400 units) at 37C on rocking platform by incubating overnight. The interacting chromatin fragments end were labeled with biotin-14-dCTP, isolated and blunt-end ligated. The proximal DNA fragments were re-ligated by ligation enzyme. The nuclear complexes were removed with proteinase K at 65C. DNA was purified by using phenol and chloroform. Biotin-C was removed from no-ligated chromatin fragments end with T4 DNA polymerase. Then, the ligated fragments were sonicated into sheared fragments of 200-600 bp in length. The biotin-labeled fragments were specifically enriched using streptavidin C1 magnetic beads. After that, A-tails were added to the fragment ends by Klenow (exo-) and Illumina paired-end sequencing adapters were ligated to collected DNA fragments. The final libraries were amplified by PCR (12-14 cycles) and sequenced on Illumina HiSeq X Ten instrument (in PE 100 bp mode).