Analysis of the DNA topology upon multiple histone H1 variants depletion by Hi-C experiments

The combined depletion of histones H1.2 and H1.4 in T47D-MTVL human breast cancer cells has a strong deleterious effect, deregulates gene expression, promotes the appearance of genome-wide accessibility sites, and triggers the interferon response. We have further analyzed the consequences of multiple H1 variants depletion at the topological level by performing Hi-C experiments on T47D-MTVL cancer cells expressing a Dox-inducible shRNA against multiple H1 variants. Overall design: Stable breast cancer-derived cell lines expressing an shRNA against different histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the presence or absence of Dox. Three Hi-C libraries were subsequently prepared and high-throughput sequenced.