The development and application of LIMe-Hi-C to simultanteously study lamina association, DNA methylation and chromosome conformation at baseline and upon EZH2 and DNMT1 inhibition

We developed and performed LIMe-Hi-C in order to assess lamina association, DNA methylation, and chromosome conformation in one experimental workflow. We combined LIMe-Hi-C with chemcial inhibition of EZH2 and DNMT1 to better understand the influence of H3K27me3 and DNA methylation on 3D genome organization. Overall design: LIMe-Hi-C experiments were performed in triplicate for FLAG-NLS-M.CviPI-Lamin-B1 K562 cells. A no doxycycline triplicate condition was included as a control to assess the specificity of the lamina association signal. EZH2 inihibtion, DNMT1 inhibition and vehicle (DMSO) treatment were each performed in triplicate for 72 hours with doxycycline added for the final 24 hours of the drug treatment. The DMSO + doxyxline condition was utilized as a control. An in situ Hi-C experiment in singlicate for the DMSO + doxycyline condition was included as quality control for the bisulfite Hi-C workflow.