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Updated: May 20, 2025
Large-scale Zebrafish Embryonic Heart Dissection for Transcriptional Analysis
Published on: January 12, 2015
Integrated single-cell transcriptome and comparative genome analysis reveals the origin of intermuscular bones in
Weidong Ye1, Mijuan Shi2, Yingyin Cheng2
1State Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Department of Vascular Surgery, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China.
Abstract:
The evolutionary process of intermuscular bones (IBs) is complex, the molecular regulatory mechanisms of their development are not clear, and even the genes involved in the evolution and development of IBs are poorly understood. In this study, comparative genomic analysis of four fish species with IBs and eleven fish species without IBs identified 106 genes that are more conservatively evolved in fish species with IBs, but highly variable in fish species without IBs. These genes are mainly involved in swimming behavior and BMP signaling pathways. We performed single-cell transcriptome sequencing of IBs origin tissues in zebrafish before and after IBs formation and found that osteoblasts and mesenchymal stem cells (MSCs) increased significantly after IBs formation. RNA velocity analysis showed that osteoblasts in IBs differentiate from MSCs, and the differentiation trajectory of MSCs into osteoblasts was successfully constructed by pseudo-time analysis. Combined with the results of multi-omics analysis, seven candidate genes associated with IBs development were screened and knocked out in zebrafish. It was found that foxn3 mutation resulted in a delay in IB development, whereas bmp6 mutation resulted in a total loss of IB. By comparing the transcriptome of IBs tissues between bmp6+/+ zebrafish and bmp6-/- zebrafish, we found that bmp6 deletion may inhibit the differentiation of MSCs into osteoblasts while promoting the formation of osteoclasts and ultimately inhibiting the formation of IBs. This study provides new insights into the molecular regulatory mechanisms and evolutionary processes of IB development.
