Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis

• Published in: Developmental cell Vol. 57; no. 10; pp. 1284 - 1298.e5
• Main Authors: Liu, Chang, Li, Rui, Li, Young, Lin, Xiumei, Zhao, Kaichen, Liu, Qun, Wang, Shuowen, Yang, Xueqian, Shi, Xuyang, Ma, Yuting, Pei, Chenyu, Wang, Hui, Bao, Wendai, Hui, Junhou, Yang, Tao, Xu, Zhicheng, Lai, Tingting, Berberoglu, Michael Arman, Sahu, Sunil Kumar, Esteban, Miguel A., Ma, Kailong, Fan, Guangyi, Li, Yuxiang, Liu, Shiping, Chen, Ao, Xu, Xun, Dong, Zhiqiang, Liu, Longqi
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 23.05.2022
• Subjects: Animals; Embryo, Mammalian; embryonic development; Embryonic Development - genetics; Gene Expression Profiling; Gene Expression Regulation, Developmental; scRNA-seq; spatial transcriptomics; Stereo-seq; Transcriptome; zebrafish; Zebrafish - genetics; Stereo-seq; scRNA-seq; zebrafish; spatial transcriptomics; embryonic development
• ISSN: 1534-5807; 1878-1551; 1878-1551
• DOI: 10.1016/j.devcel.2022.04.009

A major challenge in understanding vertebrate embryogenesis is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell-fate decisions. Here, we employed Stereo-seq to profile 91 zebrafish embryo sections covering six critical time points during the first 24 h of development, obtaining a total of 152,977 spots at a resolution of 10 × 10 × 15 μm3 (close to cellular size) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrated analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell-fate transitions and molecular changes during zebrafish embryogenesis. We further investigated the spatial distribution of ligand-receptor pairs and identified potentially important interactions during zebrafish embryo development. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development. [Display omitted] •Stereo-seq is used to generate a ZESTA•Co-varying spatial gene modules reveal the interactions between functional regions•Integration of Stereo-seq and scRNA-seq builds spatial developmental trajectories•Spatiotemporal ligand-receptor dynamics provides insights to regulatory mechanisms Liu et al. employ Stereo-seq to dissect the spatiotemporal transcriptomic dynamics in developing zebrafish embryos. This study provides a spatially resolved resource for the research of vertebrate embryogenesis and also helps to uncover how molecular and cellular interactions contribute to zebrafish embryogenesis.