Mitochondrial-generated G-quadruplex-forming lncRNAs regulate heme homeostasis

Heme is an essential but potentially toxic prosthetic group synthesized in mitochondria. Maintaining mitochondrial heme homeostasis requires precise regulation of labile heme availability. Here, we show that mitochondria-generated long non-coding RNAs (mt-lncRNAs) are enriched in G-quadruplex-forming sequences and that these RNA G-quadruplex (rG4) structures bind and buffer heme. Using G4-specific pull-down and bio-orthogonal imaging, we demonstrate rG4 formation in mt-lncRNAs inside cells and show that mt-lncRNA rG4s bind hemin in vitro . Using orthogonal chemical perturbations—a mitochondria-targeted pyrrole-imidazole polyamide (MITO-PIP), which depletes mt-lncRNAs by inhibiting L-strand transcription, and MITO-pyridostatin derivative (MITO-PyPDS), which competitively displaces heme from rG4 structures—combined with genetically encoded heme sensors and ρ0 cells, disrupting mt-lncRNA rG4s increased labile mitochondrial heme, elevated nuclear and cytoplasmic heme, induced reactive oxygen species, and upregulated heme oxygenase 1 (HMOX-1). These findings establish an RNA structure-based mechanism for organellar metabolite buffering, with implications for heme-related disorders and mitochondrial disease.