title: Microarray meta-analysis identifies evolutionarily conserved BMP signaling targets in developing long bones.
abstract: In vertebrates, BMP signaling has been demonstrated to be sufficient for bone formation in several tissue contexts. This suggests that genes necessary for bone formation are expressed in a BMP signaling dependent manner. However, till date no gene has been reported to be expressed in a BMP signaling dependent manner in bone. Our aim was to identify such genes. On searching the literature we found that several microarray experiments have been conducted where the transcriptome of osteogenic cells in absence and presence of BMP signaling activation have been compared. However, till date, there is no evidence to suggest that any of the genes found to be upregulated in presence of BMP signaling in these microarray analyses is indeed a target of BMP signaling in bone. We wanted to utilize this publicly available information to identify candidate BMP signaling target genes in vivo. We performed a meta-analysis of six such comparable microarray datasets. This analysis and subsequent experiments led to the identification of five targets of BMP signaling in bone that are conserved both in mouse and chick. Of these Lox, Klf10 and Gpr97 are likely to be direct transcriptional targets of BMP signaling pathway. Dpysl3, is a novel BMP signaling target identified in our study. Our data demonstrate that Dpysl3 is important for osteogenic differentiation of mesenchymal cells and is involved in cell secretion. We have demonstrated that the expression of Dpysl3 is co-operatively regulated by BMP signaling and Runx2. Based on our experimental data, in silico analysis of the putative promoter-enhancer regions of Bmp target genes and existing literature, we hypothesize that BMP signaling collaborates with multiple signaling pathways to regulate the expression of a unique set of genes involved in endochondral ossification.
authors.affiliation: Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India.
authors.forename: Paritosh
authors.initials: P
authors.lastname: Prashar
authors.affiliation: Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India.
authors.forename: Prem Swaroop
authors.initials: PS
authors.lastname: Yadav
authors.affiliation: Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India.
authors.forename: Fnu
authors.initials: F
authors.lastname: Samarjeet
authors.affiliation: Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, Uttar Pradesh, India. Electronic address: abandopa@iitk.ac.in.
authors.forename: Amitabha
authors.initials: A
authors.lastname: Bandyopadhyay
mesh_terms: D000818:Animals; D001483:Base Sequence; D001846:Bone Development / Q000235:genetics*; D019485:Bone Morphogenetic Proteins / Q000378:metabolism*; D001842:Bone and Bones / Q000166:cytology / Q000378:metabolism*; D002454:Cell Differentiation / Q000235:genetics; D002642:Chick Embryo; D003198:Computer Simulation; D017124:Conserved Sequence; D030541:Databases, Genetic; D019143:Evolution, Molecular; D018507:Gene Expression Regulation, Developmental; D020868:Gene Silencing; D059630:Mesenchymal Stem Cells / Q000166:cytology / Q000378:metabolism; D051379:Mice; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D010012:Osteogenesis / Q000235:genetics; D015398:Signal Transduction / Q000187:drug effects* / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D019485:Bone Morphogenetic Proteins; C526904:Dpysl3 protein, mouse; D009419:Nerve Tissue Proteins
keywords: BMP signaling; Chicken; Conditional knockout mouse; Endochondral ossification; Microarray meta-analysis; RNAi; Target genes