Context-Dependent Regulation of Microhomology-Mediated End Joining in Normal Tissues: Insights into Tissue-Specific Activation of DNA Repair Pathways

Microhomology-mediated end joining (MMEJ) is a mutagenic DNA double-strand break (DSB) repair pathway, typically regarded as a backup mechanism in cancer, activated when canonical repair pathways such as non-homologous end joining (c-NHEJ) or homologous recombination (HR) are compromised. While MMEJ has been detected in normal tissues, its presence is puzzling given its error-prone nature, and its physiological role remains poorly defined. Recent studies implicating MMEJ in mitosis suggest a potential function in normal proliferative cells. Here, we show that MMEJ is not uniformly active across tissues but is selectively enriched in proliferative tissues, including thymus, spleen, testes, and liver, while markedly reduced in post-mitotic tissues such as brain, heart, kidney, and lung. This differential activity is supported by tissue-specific expression of key MMEJ components (e.g., Ligase III, MRE11, XRCC1, PARP1, Pol θ) and inhibitory factors (e.g., WRN, RAD51, ATM). Moreover, proliferative tissues preferentially utilize short microhomologies (∼10 nt), whereas post-mitotic tissues rely on longer microhomologies (≥13 nt), indicating a shift in repair pathway choice. These findings reveal that MMEJ is a tightly regulated, context-dependent repair pathway. Its activity is tolerated in proliferative tissues due to ongoing cell turnover, while its suppression in long-lived, post-mitotic cells is likely essential to preserve genomic stability. This study assigns a physiological role to MMEJ in healthy tissue homeostasis and highlights its relevance for designing targeted DNA repair-based therapeutic strategies across diverse tissue types.