Expression analysis of INO80 complex in HepG2 liver cancer cells [RNA-seq]

We carried out two sets of experiments to understand how the INO80 complex affected gene expression. Expression analysis following depletion of INO80 with two siRNAs to determine INO80 dependent transcription programs. In addition siMCRS1 or siNTG expression analysis with and without treatment with EZH2 inhibitor (EPZ-6438) was performed to determine what genes in HepG2 cells are de-repressed by EZH2 inhibition, and test the hypothesis that changes at INO80 autonomous sites would depdend on expression of other INO80 subunits (MCRS1). We found that de-repression caused by EZH2 inhbition was blunted when cells were treated with an siRNA targeting MCRS1 and that this was especially pronounced at a set of INO80 target genes. HepG2 cells were treated with siRNA against INO80, MCRS1, or with 1uM EPZ-6438 H3K27me3 inhibitor and subjected to RNAseq.