BAP1 inhibits the ER stress gene regulatory network and modulates metabolic stress response

BRCA1 associated protein 1 (BAP1) is a tumor suppressor with de-ubiquitinating (DUB) enzyme activity and has been implicated in chromatin regulation of gene transcription. The goal of this study is to identify BAP1-dependent transcriptional alterations under both basal (25 mM glucose) and glucose starvation (0 mM glucose) conditions. To this end, we established UMRC6 cell lines (a BAP1 deficient renal cancer cell line) stably expressing Flag-tagged BAP1 wild-type (U6-F), and the empty vector control cells (U6-EV), and performed RNA sequencing (RNA-Seq) analysis in U6-EV and U6-F stable cell lines at 0, 4, and 8 hour upon glucose starvation. The RNA-Seq datasets allow us to compare BAP1-dependent transcriptional alterations under both basal and glucose deprivation conditions. Two cell line described above (U6-F: UMRC6 cells with stable expression of Flag-BAP1, and U6-EV: UMRC6 cells with stable expression of empty vector) were cultured under three conditions: T0 (cell cultured in 25mM glucose-containing medium for 8 hours), T4 (cells cultured in 0 mM glucose-containing medium for 4 hours), and T8 (cells cultured in 0 mM glucose-containing medium for 8 hours). The samples (Two replicates per cell line per condition) were then subjected to RNA sequencing analysis.