DNA methyltransferase 1-targeting miRNA-148a of dairy milk: a potential bioactive modifier of the human epigenome

Bodo C. Melnik, Gerd Schmitz

Abstract


Background: The perception of milk has changed from a “simple food” to a more sophisticated bioactive functional signaling system that promotes mTORC1-driven postnatal anabolism, growth, and development of the newborn infant. Accumulating evidence supports the view that milk´s miRNAs significantly contribute to these processes. The most abundant miRNA of milk found in milk fat and milk exosomes is miRNA-148a, which targets DNA methyltransferase 1 (DNMT1), a pivotal epigenetic regulator that suppresses transcription. Furthermore, milk-derived miRNA-125b, miRNA-30d, and miRNA-25 target TP53, the guardian of the genome that interacts with DNMT1 and regulates metabolism, cell kinetics, and apoptosis. Thus, the question arose whether cow´s milk-derived miRNAs may modify epigenetic regulation of the human milk consumer. 

Methods: To understand the potential impact of dairy milk consumption on human epigenetics, we have analyzed all relevant research-based bioinformatics data related to milk, milk miRNAs, epigenetic regulation, and lactation performance with special attention to bovine miRNAs that modify gene expression of DNA methyltransferase 1 (DNMT1) and p53 (TP53), the two guardians of the mammalian genome. By means of translational research and comparative functional genomics, we investigated the potential impact of cow´s milk miRNAs on epigenetic regulation of human DNMT1, TP53, FOXP3, and FTO, which are critically involved in immunologic and metabolic programming respectively. miRNA sequences have been obtained from mirbase.org. miRNA-target site prediction has been performed using TargetScan release 7.0.

Results: The most abundant miRNA of cow´s milk is miRNA-148a, which represents more than 10% of all miRNAs of cow´s milk, survives pasteurization and refrigerated storage. The seed sequence of human and bovine miRNA-148a-3p is identical. Furthermore, human and bovine DNMT1 mRNA share 88% identity. The miRNA-148a 7mer seed is conserved in human and bovine DNMT1 mRNA respectively, which may allow for the strong binding of bovine miRNA-148a to human DNMT1 mRNA. Consequently, we hypothesize that bovine milk miRNA-148a - protected by highly resistant milk exosome membranes - may reach the systemic circulation of the milk consumer targeting and suppressing human DNMT1 mRNA. Attenuated DNMT1 expression associated with reduced CpG promoter methylation upregulates gene expression of developmental genes such as FOXP3 and FTO. Milk-derived miRNA-125b, miRNA-30d, and miRNA-25 via targeting TP53 may downregulate p53, which physically interacts with and stabilizes DNMT1. Enhancement of dairy lactation performance is associated with increased expression of bovine milk miRNA-148a, a modification that may further increase the miRNA-148a load of dairy milk.

Conclusions: Translational evidence and comparative functional genomics support our hypothesis that bovine milk miRNA signaling may suppress human DNMT1-mediated epigenetic regulation and p53 signaling, which closely interacts with the epigenetic and transcriptional regulation of growth, metabolism, cell cycle progression, and apoptosis. Human and bovine milk miRNAs are able to target DNMT1 and TP53 mRNAs, share identical seed sequences, and resist pasteurization. Pasteurization and refrigeration of dairy milk conserves the gene regulatory software of milk and allows its unrestricted entry into the human food chain. The continued exposure of modern humans to milk´s epigenetic machinery since the widespread distribution of refrigerators is a novel change of human nutrition which may promote diseases of Western civilization.

Keywords: adipogenesis, dairy, DNA methyltransferase 1, epigenetics, exosome, miRNA-148a, miRNA-125b, milk, obesity, p53, Parkinson disease, prostate cancer


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