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This study was performed to detect molecules involved in dental hard tissue formation and tooth eruption by comparing gene expression in cap stage molar germs (before eruptive movement and dental hard tissue formation) with that in root formation stage molar germs (after eruptive movement and dental hard tissue formation). DD\u2010PCR revealed that cyclophilin A (Cyp\u2010A), a potent chemoattractant for monocytes as well as a ligand for extracellular matrix metalloproteinase inducer (EMMPRIN) was expressed differentially in the two stages molar germs. The levels of Cyp\u2010A and EMMPRIN mRNA were significantly higher at the root formation stage than at the cap and crown stages of the molar germs. Immunofluorescence showed that Cyp\u2010A and EMMPRIN were expressed strongly in the follicular cells overlaying the occlusal region of the molar germs at the root formation stage. In contrast, their immunoreactivity was weak in the follicular tissues and was not region\u2010specific in molar germs at the cap stage. In addition, the MCP\u20101 and CSF\u20101 mRNA levels increased in parallel to that of Cyp\u2010A mRNA and the increased number of osteoclasts at the occlusal region. Immunoreactivity against Cyp\u2010A and EMMPRIN was also observed in the fully differentiated ameloblasts and odontoblasts. This study suggests that Cyp\u2010A and EMMPRIN play roles in the maturation of dental hard tissue and the formation of an eruption pathway. 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