Transcriptome analysis of bone development in zebrafish (Danio rerio) during cartilaginous endochondral ossification
YU Qian, GAO Jing, JI Xiao, Adelino Canario, CHEN Jie*
International Research Center for Marine Biosciences, Ministry of Science and Technology, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
Abstract: In order to study the key regulated genes networks during the bone development of zebrafish (Daniorerio), whole bones of zebrafish were stained with Alcian blue and Alizarin double staining method at 50 dpf (days post fertilization) and 65 dpf to determine the developmental stages. Total RNA of bone tissues at 50 dpf and 65 dpf was extracted for transcriptome sequencing, differential expression genes (DEGs) were obtained for GO function annotation and KEGG enrichment. Double staining results showed that zebrafish was undergoing the process of endochondral ossification at 50 dpf, and basically completed this process at 65 dpf. Transcriptome results showed that 41.44×109 of effective data were obtained at 50 dpf and 65 dpf, with 610 DEGs. The cartilage development related genes (dlx2a, foxd3, sec23b), bone mineralization regulated gene (ptk2bb) and bone cell differentiation positive regulated gene (dlx2a) were all down regulated at 65 dpf compared to 50 dpf, indicating that the bone development was relatively matured and the process of bone cell differentiation was reduced, which was consistent with the double staining results. GO function annotation and KEGG enrichment analysis showed that most of the DEGs were enriched into the metabolic networks and reproductive signaling pathways. qPCR results with six randomly selected genes verified the reliability of the transcriptome results. Together, these results suggested that in fish, metabolism, bone development and reproduction may be closely regulated like mammals. Our results provided a new entry for the study of zebrafish bone development and disease, and a new idea for establishment of a complex disease model.
2023, Vol. 38 
