Identification of long-range chromatin interactions on K562 cells using PCHiC

Gene-regulatory elements, such as enhancers, regulate the expression of genes by physical interaction with their promoters and as such play a major role in development and disease. As enhancers not necessarily regulate the most proximal gene and are further often located in large distances to the gene they regulate, it is important to define their interaction partners to inform on their regulatory potential. To do so, we used a 3C based method called PCHIC on the myeloid leukaemia (CML) cell line K562, which is one of the most studied cell lines with much publicly available data that our data can be compared to. The knowledge obtained can be used with regards to transcriptional regulation in CML cells as well as for comparison to other leukaemias. K562 cells were first treated with either DMSO or ponatinib. Subsequently, the cells were fixed and processed with the promoter capture HiC protocol as described in Schoenfelder et al (doi:10.3791/57320).