Fig. 2: SMARCB1 reconstitution affects distal enhancers of the MYC oncogene in MRT PDOs.
From: SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors
A Hi-C contact maps depicting the MYC locus including the MYC promoter and three distal regulatory regions in P103 (E-0.9 Mb; E + 1.1 Mb; E + 1.8 Mb). Left panel depicts chromatin contact in control and the right panel contacts after SMARCB1 reconstitution. Circles indicate established chromatin loops and dashed circles indicate reduced chromatin loop formation. B ATAC-seq, ChIP-seq and CUT&RUN of the indicated proteins in MRT PDO P103 with (SMARCB1 + , lower tracks) and without (Control, upper tracks) SMARCB1 expression at the MYC locus. No antibody was included as negative control for CUT&RUN tracks (BRD9 and SS18). C Waterfall plot summarizes changes of the identified chromatin loops before and after SMARCB1 reconstitution (n = 1). The E + 1.1 Mb enhancer (RhOME2) is one of the most affected loops. D Z-scores calculated for expression of MYC, cell proliferation markers and cell cycle markers in the Control and SMARCB1+ samples of the three PDOs using bulk RNA-seq11. E CellTiter-Glo assay measuring cell viability of MRT PDOs 7 days after transduction with a non-targeting shRNA (NT) or an shRNA targeting MYC, showing that knockdown of MYC leads to a decreased proliferation of the tumor PDOs. Data is represented as means ± SD (n = 3 independent experiments) (n = 3). Source data are provided as a source data file.
