Analysis of the DNA topology in T47D-MTVL cells by Hi-C data

The topology of the genome in untreated T47D-MTVL cells expressing a Dox-inducible shRNA against multiple H1 variants was analyzed by performing a Hi-C experiment. The data allowed the obtention of Hi-C chromosome interaction maps, which were used to define TADs and A/B compartments, and to study the relationship between the 3D genome in breast cancer cells and other genomic properties as well as the histone H1 variants genome-wide distribution. Overall design: Stable breast cancer-derived cells expressing an shRNA against different histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the absence of Dox. An in situ Hi-C library was subsequently prepared and high-throughput sequenced to study the 3D genome.