We identified micro RNA (miR)-1978 that may originate from the mitochondrial genome, with a nucleotide sequence that perfectly matches the partial series of DHFR, KIF5C, and MSH3 genes of the nuclear genome. Overexpression of miR-1978 in the SHSY5Y cell line reduces DHFR, KIF5C, and MSH3 mRNA and protein expression, results in a division arrest in the G1 phase of the cell cycle, the number of cells in the G2/M stage was observed to decrease, and the number of apoptotic cells increased. Cells overexpressing miR-1978 exhibit a different nuclear DNA methylation status compared to that of controls. Several Alzheimer’s disease-related proteins such as amyloid β precursor protein, Tau, p-Tau or α-synuclein (a Parkinson’s disease-related protein), were increased in SHSY5Y cells overexpressing miR-1978. Neuroid cells induced by SHSY5Y overexpressing miR-1978 using retinoic acid have been observed to lack dendritic spines.