Systematic genetic perturbation reveals principles underpinning robustness of the epigenetic regulatory network [RNA-Seq]

We profiled gene expression in iCas9-expressing HCEC-1CT and HME1 cells that were either WT or knockout for ARID1A or CREBBP, to determine the cell type variability in expression levels of epigenetic regulators and the transcriptional consequences of epigenetic regulator loss. A lentiviral dox-inducible Cas9 construct, adapted from Addgene 50661 for hygromycin resistance, was introduced to HME1 and HCEC-1CT cells. Knockout cell lines were generated by transfection of synthetic gRNA targeting ARID1A or CREBBP, and clonal lines were raised, genotyped, and pooled for final populations containing 3-6 knockout clones per line. WT lines were also generated by clonal isolation and pooling. RNA was isolated from three independent populations of healthy growing cells of each cell line, at c50% confluence and 10-20 passages within our laboratory.