Malignancy and NF-kB signalling strengthen coordination between the expression of mitochondrial and nuclear-encoded oxidative phosphorylation genes

Abstract

Mitochondria are ancient endosymbiotic organelles crucial to eukaryotic growth and metabolism. Mammalian mitochondria carry a small genome containing thirteen protein-coding genes with the remaining mitochondrial proteins encoded by the nuclear genome. Little is known about how coordination between the two sets of genes is achieved. Correlation analysis of RNA-seq expression data from large publicly-available datasets is a common method to leverage genetic diversity to infer gene co-expression modules. Here we use this method to investigate nuclear-mitochondrial gene expression coordination. We identify a pitfall in correlation analysis that results from the large variation in the proportion of transcripts from the mitochondrial genome in RNA-seq data. Commonly used normalization techniques based on total read count (such as FPKM or TPM) produce artefactual negative correlations between mitochondrial- and nuclear-encoded transcripts. This also results in artefactual correlations between pairs of nuclear-encoded genes, thus having important consequences for inferring co-expression modules beyond mitochondria. We show that these effects can be overcome by normalizing using the median-ratio normalization (MRN) or trimmed mean of M values (TMM) methods. Using these normalizations, we find only weak and inconsistent correlations between mitochondrial and nuclear-encoded mitochondrial genes in the majority of healthy human tissues from the GTEx database. However, a subset of healthy tissues with high expression of NFkB show significant coordination supporting a role for NFkB in retrograde signalling. Contrastingly, most cancer types show robust coordination of nuclear and mitochondrial OXPHOS gene expression, identifying this as a feature of gene regulation in cancer.

Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels

“…In contrast to plants, animal mitochondrial mRNAs can undergo widespread polyadenylation (45). Accordingly, standard RNA-seq datasets have been used to quantify the abundance of mitochondrial vs. nuclear mRNAs in humans, and our findings parallel observations that the 13 protein-coding genes in the human mitochondrial genome can account for ~30-50% of all mRNA transcripts in tissues with high metabolic activity such as heart and brain (20, 21).…”

“…For example, a typical diploid plant leaf cell contains two copies of the nuclear genome, dozens of copies of mitochondrial genome, and hundreds to thousands of copies of the plastid genome (14)(15)(16)(17). Nuclear and organellar mRNA transcripts may exist in imbalanced ratios (18)(19)(20)(21). For example, the mitochondrial OXPHOS genes have higher mRNA abundances than their N-mt counterparts even though the corresponding proteins are typically found in equimolar ratios within these complexes (18).…”