4C-seq of a K562 cell line model with a patient-based t(3;8) translocation

Chromosome Conformation Capture Sequencing (4C-seq) was performed to assess interaction between the MYC super-enhancer and the EVI1 promoter under different conditions. Sample preparation was performed as previously described (van de Werken et al., 2012). In short, genomic regions that are spatially proximal in the cell nucleus were fixated by formaldehyde-induced crosslinks. The DNA was fragmented with DpnII as a primary restriction enzyme, Csp6I as a secondary 4 bp-cutter. To identify and quantify fragments that were ligated to the genomic region of interest, a two-step PCR was performed as previously described (Krijger et al., 2020). In the second PCR step, universal primers were used that contain the Illumina adapters. The amplicons were analyzed using next generation sequencing on the IIlumina NovaSeq platform.