RNAseq in protected BAP1 mESc

Malignancies arising from mutation of tumor suppressor genes display an unexplained tissue proclivity. For example, tumor suppressor BAP1 encodes a ubiquitously expressed deubiquitinase for histone H2A but germline mutations predominantly cause uveal melanomas and mesotheliomas. We show that BAP1 inactivation causes apoptosis in mouse embryonic stem cells, fibroblasts, liver and pancreas, whereas melanocytes and mesothelial cells remain viable. E3 ligase RNF2, which silences genes by monoubiquitinating H2A, promoted apoptosis in BAP1-deficient cells by suppressing the pro-survival genes Bcl-2 and Mcl-1. Our data argue that BAP1 modulates gene expression by countering H2A ubiquitination, but its loss only promotes tumorigenesis in cells that do not engage an RNF2-dependent apoptotic program. We propose that intolerance of BAP1 loss, and perhaps the loss of other tumor suppressors, restricts the mutant tumor spectrum. RNA was extracted from following genotypes - BAP1 wt (WT_D4), knock-in BAP1 C91A mutant (C91A_D4_4OHT), BAP1 C91A control (C91A_D4), BAP1 knockout (cKO_D4_4OHT), BAP1 knockout control (cKO_D4),and RNF2-BAP1 double knockout (dKO_D4)) in mouse embryonic stem cells. Cultured cells were treated with Tamoxifen 100 nM 4-hydroxytamoxifen (4-OHT; EMD Millipore) for 4 days to induce Cre-mediated recombination. To preotect cells from death due to BAP1 knockout, all cells were treated with emricasan.