Brassica biased gene retention during diploidization linked to 3D genome organization

By combining Hi-C and histone modification, we provided the insights into the chromatin architecture and its implications for function and evolution Two grams of harvested leaves per accessions was sampled and then cross-linked with 1% formaldehyde in a vacuum for 15 min. After crosslinking was stopped with 0.125 M glycine under a vacuum for12 min, the extracted chromatin of these crosslinked tissue sles was sonicated to 100-300 bp. With protein G beads, the proteins of interest were pulled down by adding a specific antibody to H3K4me3 (Abcam; ab8580), H3K27me3 (CST; 9733S), and H3K9ac (CST; 9649). The DNA binding to the protein of interest was harvested by digesting the protein with proteinase K. The input DNA was also purified as a control20, 59. The ChIP libraries were constructed following the protocol of the NEXTflex® Rapid DNA-Seq Kit and sequenced on Illumina HiSeq X-Ten with the PE 150 method.