Transcriptome analysis of early chondrogenesis in ATDC5 cells induced by bone morphogenetic protein 4.

We performed serial analysis of gene expression (SAGE) profiling in mouse chondrogenic ATDC5 cells before and 6 h after the onset of chondrogenesis induced by BMP4. A total of 43,656 SAGE tags (21,875 and 21,781 tags from the uninduced and induced libraries, respectively) were analyzed. Our analysis predicted that 139 transcripts were differentially represented in the two libraries (p < 0.05), including 72 downregulated and 67 upregulated transcripts. Ninety-five of them matched single UniGene entries (77 known genes and 18 ESTs), while 12 tags corresponded to potentially novel genes. Surprisingly, many of these known genes have never been implicated in chondrogenic differentiation. Interestingly, we found that a significant fraction of these genes formed physical linkage groups. This suggests that the transcriptional control by BMP signaling is in part targeted to genes in certain chromosomal domains. Together, our results provide novel insights into molecular events regulated by BMP signaling in chondrogenesis.