Hypoxia leads to reduced mito-nuclear gene expression and increased mtDNA transcriptional pausing in human cells

Mitochondria respond to various stresses. Nevertheless, the regulation of this response while considering coordination between mitochondrial (mtDNA)- and nuclear DNA (nDNA)-encoded gene expression has been overlooked. Our RNA-seq analysis of 18 human cell lines grown in hypoxia (0.2-2% oxygen, 16-24 h) reveals a significant and coordinated reduction of mito-nuclear oxidative phosphorylation (OXPHOS) genes' expression in most (N = 11) cell lines. mtDNA copy number assessment in U87, HCT-116, MCF-7, and HeLa cells reveals non-significant changes, suggesting that the overall reduced mito-nuclear gene expression (MNGE) in hypoxia occurs at the RNA level. Analysis of HIF1α ChIP-seq experiments from cells exposed to hypoxia reveals increased binding to upstream regulatory elements of certain regulators of mitochondrial gene expression. Furthermore, RNA-seq analysis of HIF1α knockout HCT-116 cells grown in hypoxia reveals reduced mtDNA gene expression, yet no change in nDNA OXPHOS genes, suggesting that HIF1α knockout led to departure from coordination of MNGE. Finally, nascent RNA transcripts analysis (PRO-seq) in HeLa, U87, and D407 cells grown in hypoxia shows increased intensity of pausing sites throughout the mtDNA. This finding suggests an important role for transcriptional pausing in the regulation of mtDNA gene expression. Taken together, coordinated reduction of MNGE in hypoxia underlines MNGE as a pivotal player in general mitochondrial function, and particularly in response to stress.