Nuclear genetic regulation of human mitochondrial RNA modification

Abstract

RNA modifications affect the stability and function of RNA species, regulating important downstream processes. Modification levels are often dynamic, varying between tissues and individuals, although it is not always clear what modulates this variation or what impact it has on biological systems. Here, we quantify variation in RNA modification levels at functionally important positions in the mitochondrial genome across 11,552 samples from 39 tissue/cell types and find evidence that modification levels impact mitochondrial transcript processing. We identify novel links between mitochondrial RNA modification levels in whole blood and genetic variants in the nuclear genome, including missense mutations in LONP1 and PNPT1, as well as missense mutations in MRPP3, SLC25A26 and MTPAP that associate with RNA modification levels across multiple tissue types. Genetic variants linked to modification levels are associated with multiple disease phenotypes, including blood pressure, breast cancer and Moyamoya disease, suggesting a role for these processes in complex disease.