BRG1 shRNA knockdown in ALCL cell lines

To determine the consequences of Brg1 expression in ALCL, cells were transfected with shRNA to Brg1 leading to a decrease in Brg1 transcript and protein levels. RNA was isolated 72 hours later from the shRNA5 (TRCN0000015551) expressing cells and sequencing conducted to examine changes to the transcriptome mediated by Brg1. Following differential gene expression analysis of the scrambled shRNA versus shRNA5, the transcriptome was identified as being dramatically altered showing both downregulation (2,527 mRNA transcripts: of a cumulative 26,833 genes, adj. p ≤ 0.05) and upregulation (2,900 mRNA transcripts, of a cumulative 26,833 genes, adj. p ≤ 0.05) of genes. When analysing the the 15,285 protein-coding genes alone, 1,934 (13%) were downregulated while 2,797 (18%) were upregulated (adj. p ≤ 0.05). To establish which physiological processes are most affected by the activity of BRG1, pathway enrichment analyses were undertaken. The input comprised of the significant (adj. p ≤ 0.05) protein-coding targets, where the absolute log2 fold change of expression was ± 1.5. Transcripts whose expression was either induced (n=33) or repressed (n=243) by BRG1 were investigated. Reactome analysis suggests that BRG1 plays roles in upregulating genes associated with the cell cycle, while suppressing genes associated with epigenetic regulation.