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Background  The runt-related transcription factor 2 (Runx2) is a cell-fate-determining factor that controls osteoblast differentiation and bone formation. It has been previously demonstrated that microRNAs (miRNAs) play important roles in osteogenesis. However, the Runx2-regulated miRNAs that have been reported thus far are limited. In this study, we pursued to identify these miRNAs in Tet-on stable C2C12 cell line (C2C12/Runx2 Dox  subline).    Results  Microarray analysis revealed that alterations in miRNA expression occur with 54 miRNAs. Among these miRNAs, miR-690 was identified as a positive regulator of Runx2-induced osteogenic differentiation of C2C12 cells through gain- and loss-of-function assays. Expression of miR-690 is induced by Runx2, which binds directly to the putative promoter of  mir - 690  ( Mirn690 ). The miR-690 proceeds to inhibit translation of the messenger RNA encoding the nuclear factor kappa B (NF-κB) subunit p65 whose overexpression inhibits Runx2-induced osteogenic differentiation of C2C12 cells. Interleukin-6 (IL-6), a downstream target of NF-κB pathway, is upregulated by p65 overexpression but significantly downregulated during this differentiation process. Furthermore, overexpression of IL-6 impedes the expression of  osteocalcin , a defined marker of late osteoblast differentiation.    Conclusions  Together, our results suggest that the miR-690 transactivated by Runx2 acts as a positive regulator of Runx2-induced osteogenic differentiation by inactivating the NF-κB pathway via the downregulation of the subunit p65.    Electronic supplementary material  The online version of this article (doi:10.1186/s13578-016-0073-y) contains supplementary material, which is available to authorized users.

MiR-690, a Runx2-targeted miRNA, regulates osteogenic differentiation of C2C12 myogenic progenitor cells by targeting NF-kappaB p65