Hypoxia leads to unique mtDNA transcriptional patterns and affects mito-nuclear regulatory coordination

Mitochondria is a central player in cellular metabolism, cell life, and death. Unlike all cellular functions, the mitochondria are operated by a unique bi-genomics system that involves cooperation between factors encoded by the mitochondrial genome (mtDNA) and by the nuclear genome (nDNA). Recently, we showed that such coordination is perturbed in human diseases, such as COVID19. Notably, these diseases are aggravated by exposure to environmental stresses, especially hypoxia. Therefore, we asked whether mitochondrial transcription and mito-nuclear co-expression, respond to environmental stresses. To address this question, we have grown three human cell lines (HeLa, U87, and D407) in two types of mitochondria-related stresses: either carbon source change (glucose vs galactose) or hypoxia (24hr 1% oxygen). These cells were subjected to in-vivo assessments of nascent transcription (PRO-seq), mitochondrial copy number (qPCR), and membrane potential. Our results revealed that whereas growth under galactose-based media did not result in consistent alteration of mitochondrial transcription, hypoxia did. Specifically, although mtDNA light strand transcriptional initiation was elevated in hypoxia, transcriptional elongation levels of the same strand dropped around mtDNA position ~8700 below the control in HeLa and U87 cells, but not in D407 cells. Additionally, the altered mtDNA transcription was associated with reduced transcription in nDNA-encoded OXPHOS genes, which was even more pronounced in RNA-seq. Interestingly, such changes did not associate with altered mtDNA copy number, hence suggesting a transcriptional regulatory change rather than an overall impact on mitochondrial biogenesis. The unexpected similarity in mtDNA transcriptional pattern alteration in hypoxia across cell lines suggests similarity in the underlying mechanism.