Genome-wide analysis of the effects of siRNA-mediated removal of components of ESCRT-I or HOPS complexes on gene expression in HEK293 cells

To identify genes regulated by ESCRT-I or HOPS complexes, whole-genome expression profiling (Illumina Human HT-12 BeadChip arrays) of cells lacking TSG101 or VPS28 (ESCRT-I components) or VPS11, VPS39 or VPS41 (HOPS components) was performed. We found that loss of ESCRT-I activates the expression of inflammatory genes and genes encoding glycolytic enzymes and leads to reduced expression of genes encoding enzymes of oxidative metabolism of amino acids and fatty acids. In contrast to ESCRT-I dysfunction, inactivation of HOPS has no major impact on the cellular transcriptional program, as it leads to up-regulated expression of a relatively small number of genes, which encode mainly plasma membrane or secreted proteins.