Transcriptome analysis of early chondrogenesis in ATDC5 cells induced by bone morphogenetic protein 4 $ , $$ Matthias Wahl, a,1 Chisa Shukunami, b,1 Ulrich Heinzmann, c Kumiko Hamajima, b,2 Yuji Hiraki, b and Kenji Imai a, * a Institute of Developmental Genetics, GSF-National Research Center for Environment and Health, Ingolsta ¨dter Landstrasse 1, D-85764, Neuherberg, Germany b Department of Cellular Differentiation, Institute for Frontier Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan c Institute of Pathology, GSF-National Research Center for Environment and Health, Ingolsta ¨dter Landstrasse 1, D-85764, Neuherberg, Germany Received 25 February 2003; accepted 5 June 2003 Abstract 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. D 2003 Elsevier Inc. All rights reserved. Keywords: Chondrogenesis; BMP4; ATDC5; Transcriptome; SAGE Axial and appendicular skeletons of higher vertebrates form via a multistep process called endochondral bone formation in which cartilaginous rudiments are replaced by bone [1]. In developing embryos, mesenchymal pre- cursor cells of somite or lateral plate mesoderm origin condense to prefigure cartilaginous rudiments of skeletal elements in response to signals from surrounding tissues [2]. Cells in the condensation areas differentiate into chondrocytes to proliferate and produce a large amount of cartilage-characteristic extracellular matrix proteins such as type II collagen and aggrecan. The cells then become hypertrophic and start to synthesize type X collagen. Next to the most advanced hypertrophic chondrocytes, calcifi- cation of cartilage occurs at the matrix around the cells and calcified cartilage is invaded by blood vessels accom- panying osteoblasts and osteoclasts that ultimately produce bony tissues. In the past years, key secreted signaling molecules that regulate endochondral bone formation have been identified [3]. Among them, bone morphogenetic proteins (BMPs) 2, 4, and 7, which are members of the TGF-h superfamily, can induce ectopic formation of cartilage and bone at the sites injected intramuscularly or subcutaneously by recruiting mesenchymal precursor cells [4,5]. Thus, BMPs are consid- ered to play a pivotal role in chondrogenic and osteogenic differentiation during endochondral bone formation. BMP signaling is received by specific serine/threonine kinase receptors consisting of two type I receptor subunits (BMPR-IA and BMPR-IB) and two type II receptor sub- units (BMPR-II) and is transduced to the nucleus by Smad proteins [6]. During embryonic development, Bmp2 and Bmp4 are expressed in mesenchyme precursor cells prior to condensation and also later in the perichondrium [7,8]. 0888-7543/$ - see front matter D 2003 Elsevier Inc. All rights reserved. doi:10.1016/S0888-7543(03)00201-5 $ SAGE data from this article have been deposited with the Gene Expression Omnibus under Accession Nos. GSM2575 and GSM2576. $$ Supplementary data associated with this article can be found at doi:10.1016/S0888-7543(03)00201-5. * Corresponding author. Fax: +49-89-3187-3099. E-mail address: imai@gsf.de (K. Imai). 1 These two authors contributed equally to this work. 2 Present address: Department of Neuroscience, Osaka Bioscience Institute, Suita, Osaka 565-0874, Japan. www.elsevier.com/locate/ygeno Genomics 83 (2004) 45 – 58