Genome-wide chromatin interactions identify characteristic promoter-distal loops

We developed a novel computational model, HiSIF (Hi-C Significant Interacting Fragments), which uses a Poisson Mixture Model (PMM) with a power-law decay background. We compared its performance to some existing programs with publicly available Hi-C data, and then applied it to in situ Hi-C data in breast cancer sensitive and resistant cells. Overall design: In this study, we tested the model in our newly generated Hi-C data in three ERa positive breast cancer cell lines, MCF7, tamoxifen-resistant MCF7 (MCF7-TamR) (MCF7 and MCF7-TamR data have been deposited in GEO under accession number GSE108787), T47D and tamoxifen-resistant T47D (T47D-TamR), ZR75-1 and tamoxifen-resistant ZR75-1 (ZR75-1-TamR).