Mitochondrial DNA methylation: State-of-the-art in molecular mechanisms and disease implications

BACKGROUND: Mitochondrial DNA (mtDNA), a circular genome essential for cellular energy production, is increasingly recognized to exhibit aberrant methylation under pathological conditions. Dysregulated methylation in regulatory regions can impair mtDNA replication, transcription, and metabolic homeostasis, thereby promoting disease progression, including neurodegenerative diseases, cardiovascular diseases, metabolic disorders, as well as aging. Despite challenges posed by nuclear pseudogene interference, advanced detection technologies have significantly improved the resolution of mtDNA methylation analysis. AIM OF REVIEW: This review focuses on three key mtDNA methylation patterns, 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and N6-methyladenine (6mA), summarizing the evidence for their existence as well as their molecular mechanisms in diseases and offering insights into recent advances in mtDNA detection techniques. Key Scientific Concepts of Review: Under pathological conditions, the dysregulation of mtDNA methylation highlights its emerging promise as both a biomarker and therapeutic target. Therefore, this epigenetic aberration provides a foundational framework for elucidating the molecular mechanisms underlying mitochondrial dysfunction across diverse diseases and advancing precision medicine strategies.