The ventricular-subventricular zone harbors neural stem cells (NSCs) that can differentiate into neurons, astrocytes, and oligodendrocytes. This process requires loss of stem cell properties and gain of characteristics associated with differentiated cells. miRNAs function as important drivers of this transition; miR-124, -128, and -137 are among the most relevant ones and have been shown to share commonalities and act as proneurogenic regulators. We conducted biological and genomic analyses to dissect their target repertoire during neurogenesis and tested the hypothesis that they act cooperatively to promote differentiation. To map their target genes, we transfected NSCs with antagomiRs and analyzed differences in their mRNA profile throughout differentiation with respect to controls. This strategy led to the identification of 910 targets for miR-124, 216 for miR-128, and 652 for miR-137. The target sets show extensive overlap. Inspection by gene ontology and network analysis indicated that transcription factors are a major component of these miRNAs target sets. Moreover, several of these transcription factors form a highly interconnected network. Sp1 was determined to be the main node of this network and was further investigated. Our data suggest that miR-124, -128, and -137 act synergistically to regulate Sp1 expression. Sp1 levels are dramatically reduced as cells differentiate and silencing of its expression reduced neuronal production and affected NSC viability and proliferation. In summary, our results show that miRNAs can act cooperatively and synergistically to regulate complex biological processes like neurogenesis and that transcription factors are heavily targeted to branch out their regulatory effect. STEM CELLS 2016;34:220-232
SIGNIFICANCE STATEMENTWe demonstrate here, perhaps for the first time, that miRNAs (miR-124, -128 and -137) can act cooperatively to regulate a complex biological problem such as neurogenesis. They do so by targeting overlapping sets of genes. Moreover, our genomic analyses determined that transcription factors are the main component of their target sets. Our results indicate additional associations between the three analyzed miRNA and the targeted TFs. Based on described ChIP analysis, we suggest that miR-124, -128 and -137 and their targeted TFs could act on overlapping and related target sets producing different functional outcomes that ultimately would influence the balance self-renewal/differentiation.