Small but mighty: mitochondrial DNA at the centre of retrograde signalling

Mitochondria form highly dynamic and interconnected networks that continuously communicate with the cytoplasm and the nucleus to maintain cellular homeostasis and coordinate adaptive responses to stress. This bidirectional communication, known as mito-nuclear crosstalk, is essential for regulating metabolism, redox balance, immune activation, and cell fate decisions. While retrograde signalling has traditionally been viewed as a consequence of metabolic or oxidative perturbations, mounting evidence positions mitochondrial DNA (mtDNA) as a central and active regulator of these signalling pathways. Beyond encoding essential subunits of the electron transport chain, mtDNA functions as a signalling hub that conveys information about mitochondrial functional status to the nucleus. Perturbations in mtDNA integrity, copy number, or expression initiate retrograde responses through metabolic rewiring, alterations in redox and calcium signalling, and activation of stress-responsive transcriptional programmes. In addition, mtDNA-derived products, including mitochondrial-derived non-coding RNAs (mt-ncRNAs) and mitochondrial-derived peptides (MDPs), have emerged as key messengers that shuttle between cellular compartments, reshape nuclear gene expression, and influence cellular and systemic responses to stress. These molecules participate in diverse processes, ranging from mitochondrial biogenesis and quality control to innate immune activation and epigenetic regulation. This review synthesises current knowledge on mtDNA-driven retrograde signalling, highlighting both classical and emerging mechanisms by which the mitochondrial genome communicates with the nucleus. We discuss how mtDNA instability, defective repair, and altered mitochondrial dynamics trigger signalling cascades involving metabolic sensors, calcium fluxes, and innate immune pathways. We further examine the growing evidence supporting regulatory roles for mt-ncRNAs, including small RNAs, long non-coding RNAs, double-stranded RNAs, and circular RNAs, as well as MDPs such as Humanin, SHLPs, and MOTS-c, in coordinating adaptive nuclear responses. By integrating these diverse signalling modalities, this review highlights mtDNA as an integral and active signalling platform that coordinates mitochondrial stress sensing with nuclear adaptive responses.