Single-cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-genesis in Pigs

• Published in: Genomics, proteomics & bioinformatics Vol. 19; no. 3; pp. 423 - 436
• Main Authors: Li, Jianbo, Wang, Ligang, Yu, Dawei, Hao, Junfeng, Zhang, Longchao, Adeola, Adeniyi C., Mao, Bingyu, Gao, Yun, Wu, Shifang, Zhu, Chunling, Zhang, Yongqing, Ren, Jilong, Mu, Changgai, Irwin, David M., Wang, Lixian, Hai, Tang, Xie, Haibing, Zhang, Yaping
• Format: Journal Article
• Language: English
• Published: England Elsevier B.V 01.06.2021; State Key Laboratory of Genetic Resources and Evolution,Yunnan Laboratory of Molecular Biology of Domestic Animals,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming 650223,China; Department of Laboratory Medicine and Pathobiology,University of Toronto,Toronto,Ontario M5S1A8,Canada%State Key Laboratory for Molecular and Developmental Biology,CAS Center for Excellence in Brain Science and Intelligence Technology,Institute of Genetics and Developmental Biology,Chinese Academy of Sciences,Beijing 100101,China%State Key Laboratory of Genetic Resources and Evolution,Yunnan Laboratory of Molecular Biology of Domestic Animals,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming 650223,China; Kunming College of Life Science,University of Chinese Academy of Sciences,Kunming 650223,China%Institute of Animal Science,Chinese Academy of Agricultural Sciences,Beijing 100193,China%State Key Laboratory of Stem Cell and Reproductive Biology,Institute of Zoology,Chinese Academy of Sciences,Beijing 100101,China%Core Facility for Protein Research,Institute of Biophysics,Chinese Academy of Sciences,Beijing 100101,China%State Key Laboratory of Genetic Resources and Evolution,Yunnan Laboratory of Molecular Biology of Domestic Animals,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming 650223,China%State Key Laboratory of Genetic Resources and Evolution,Yunnan Laboratory of Molecular Biology of Domestic Animals,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming 650223,China; Center for Excellence in Animal Evolution and Genetics,Chinese Academy of Sciences,Kunming 650223,China; Kunming College of Life Science,University of Chinese Academy of Sciences,Kunming 650223,China; Elsevier
• Subjects: Angiogenesis; Animals; Original Research; Osteogenesis; Rib-genesis; Ribs; scRNA-seq; Sequence Analysis, RNA; Single-Cell Analysis; Spine; Swine - genetics; Thoracolumbar vertebra transition; Transcriptome; Thoracolumbar vertebra transition; Angiogenesis; scRNA-seq; Osteogenesis; Rib-genesis
• ISSN: 1672-0229; 2210-3244
• DOI: 10.1016/j.gpb.2021.09.008

Development of thoracolumbar vertebra (TLV) and rib primordium (RP) is a common evolutionary feature across vertebrates, although whole-organism analysis of the expression dynamics of TLV- and RP-related genes has been lacking. Here, we investigated the single-cell transcriptome landscape of thoracic vertebra (TV), lumbar vertebra (LV), and RP cells from a pig embryo at 27 days post-fertilization (dpf) and identified six cell types with distinct gene expression signatures. In-depth dissection of the gene expression dynamics and RNA velocity revealed a coupled process of osteogenesis and angiogenesis during TLV and RP development. Further analysis of cell type-specific and strand-specific expression uncovered the extremely high level of HOXA10 3′-UTR sequence specific to osteoblasts of LV cells, which may function as anti-HOXA10-antisense by counteracting the HOXA10-antisense effect to determine TLV transition. Thus, this work provides a valuable resource for understanding embryonic osteogenesis and angiogenesis underlying vertebrate TLV and RP development at the cell type-specific resolution, which serves as a comprehensive view on the transcriptional profile of animal embryo development.