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Abstract: Microbial polyhydroxyalkanoates (PHA) including poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx) were found to induce chondrogenesis of mesenchymal stem cells (MSCs) and preserve chondrocytic phenotype as well as support chondrocytes-specific extracellular matrix (ECM) secretion. In this study, mouse MSCs cultured on the PHBHHx films for 24 h showed up-regulated expression of chondrogenic marker genes including aggrecan, col2, sox9, col10 and pthrp. To further illustrate this phenomonon, chondrogenesis-related microRNA expression profiling was examined by quantitative real-time PCR (RT-PCR) based on results of microRNA array obtained from comparison between mouse MSCs and mature mouse chondrocytes. Among 44 microRNAs related to chondrogenesis on microrray studies, considering only broadly-conserved microRNAs, seven differentially-expressed microRNAs were selected to study their target genes related to chondrogenesis. Two microRNAs out of the seven, namely, miR-29a and miR-29b, were revealed to directly target 3′ UTR of col2a1 encoding type II collagen by dual-luciferase assay, and their activity was under the regulation of Sox9, the SRY-related high mobility group-box gene 9. For the first time microRNAs were shown to regulate the stem cell differentiation processes mediated by cell–material interactions. [Copyright &y& Elsevier]