3D gene regulation network in glioma ferroptosis
Erastin is a small molecular compound which inhibits the system Xc- and prevents the import of cystine, reducing glutathione (GSH) biosynthesis and glutathione peroxidase 4 (GPX4) activity, and finally inducing cell death via ferroptosis. To establish a model of Erastin induced ferroptosis in glioma cells, U87 cells were treated of Erastin (10 µM, 72 h). Combination analysis of HiChIP, ChIP-seq and RNA-seq data suggests that change of chromatin loops mediated by 3D chromatin structure regulate gene expressions in glioma ferroptosis. Genes that regulated by 3D chromatin structure include genes that were reported function in ferroptosis like MDM2 and TXRND1. We propose a new regulatory mechanism governing glioma cell ferroptosis by 3D chromatin structure. Overall design: 2 biological replicates were analyzed for Erastin-treated glioma U87 cells (10 µM, 72 h) and control U87 cells by RNA-seq, 2 biological replicates of H3K27ac ChIP-seq for U87, 2 biological replicates of H3K27ac ChIP-seq for Erastin (10 µM, 72 h)-treated U87 cells, 2 biological replicates of H3K4me1 ChIP-seq for U87, 2 biological replicates of H3K4me1 ChIP-seq for Erastin (10 µM, 72 h)-treated U87 cells,  2 biological replicates of H3K27ac HiChIP for U87, 2 biological replicates of H3K27ac HiChIP for Erastin (10 µM, 72 h)-treated U87 cells.