The hepatic mitochondrial landscape

Mammalian energy homeostasis depends on coordinated metabolism across tissues, with the liver acting as a central hub for systemic energy balance and biosynthetic precursor supply. Hepatic mitochondria are integral to these functions, yet mitochondrial gene expression across liver microanatomical space remains incompletely defined. Here, we mapped the expression of genes supporting mitochondrial function at single-cell level across the feeding-fasting cycle and spatial gradients within the liver lobule in female and male mice. Hepatocyte subtypes exhibited pronounced mitochondrial divergence, including a non-canonical population characterised by low mitochondrial gene expression and reduced secretory protein production. We showed that higher periportal oxidative phosphorylation relies on an exceptionally high periportal mitochondrial transcript fraction that mirrors the mitochondrial-to-cell volume ratio, directly linking scRNA-seq read counts to mitochondrial content while also highlighting the limitations of the mitochondrial read fraction as a standalone scRNA-seq quality metric. Nuclear- and mitochondrial-encoded oxidative phosphorylation genes exhibited distinct zonation, revealing a lack of stoichiometric coordination at the transcript level. Ultrastructural reconstruction revealed zonation of mitochondrial architecture beyond size, including increased branching of periportal mitochondria. In humans, we recapitulated the higher periportal mitochondrial transcript abundance using spatial transcriptomics data. Mitochondrial gene expression rhythms, previously reported in mice, were also conserved in humans and peaked around the first meal in both species. Together, these findings reveal heterogeneity in hepatic mitochondrial biology and provide a framework for interpreting mitochondrial variation in liver single-cell studies.