Differential Gene Expression Between the Growth Plate and Non-growth Plate Forming Bones in the Mouse Carpus and Tarsus

Several bones within the developing mammalian autopod possess a growth plate on only one end. This includes the metatarsals (MT), the pisiform in the wrist, and calcaneus in the ankle. While regulation of growth plate cartilage is well understood, little is known about which genes specify where growth plates do and do not form in the skeleton. We used RNA-seq to identify differentially expressed genes (DEGs) between four tissues with a growth plate forming and non-forming region in postnatal day 4 (P4) and P9 mice: 1) proximal versus distal MT1, 2) distal versus proximal MT3, 3) pisiform versus all other carpals, and 4) proximal versus distal calcaneus. We compared DEGs that had a positive fold change and a significance value of p < 0 .05 for all four datasets within each age group to identify common genes with higher expression in the growth plate forming region. We identified 4 genes at P4 and 8 genes at P9 that met these criteria. Stra6, a member of the retinoic acid signaling pathway, was the only gene to be shared between both age groups. In situ hybridization shows Stra6 to be strongly expressed in the perichondrium adjacent to proliferative chondrocytes in growth plate and minimally expressed in the non-growth plate forming cartilage. This analysis demonstrates the utility of using variation in growth plate location to identify growth plate specific genes.