Tsukuba, Japan—Single-cell RNA sequencing (scRNA-seq) is a powerful technique that enables the comprehensive analysis of gene expression in individual cells. During embryonic development, cells within the same embryo diverge into multiple lineages and adopt distinct fates. scRNA-seq enables the capture of such cell-type-specific differences that are masked in population-averaged analyses, such as bulk RNA-seq. Nevertheless, rare cell populations—such as neurons in sea urchin embryos and larvae—are often underrepresented, thereby complicating the detailed analysis of neurogenic lineages and regulatory dynamics.
In this study, the researchers constructed a developmental scRNA-seq atlas spanning the embryogenesis of a Japanese sea urchin, Hemicentrotus pulcherrimus , from 24 to 96 h after fertilization and systematically characterized the dynamic changes in cell states at single-cell resolution. Moreover, by pharmacologically inhibiting Delta-Notch-mediated lateral inhibition to improve neuronal differentiation, the researchers were able to capture neuronal lineages and associated gene expression clusters that are difficult to detect under normal developmental conditions. All datasets have been made publicly available through the Japanese sea urchin genome database HpBase, thereby providing an accessible research platform that allows even users without bioinformatics expertise to intuitively explore gene expression patterns.
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This work was supported by JST, PRESTO Grant Number JPMJPR1945 and JSPS KAKENHI Grant Numbers 19K20406 and 23K11312 to K.T., and JST, PRESTO Grant Number JPMJPR194C, JST A-STEP Grant number JPMJTR204E, and JSPS KAKENHI Grant number 23K23933 to S.Y.
Title of original paper:
Single-cell transcriptomic resources for tracing neurogenesis and cell fate specification in sea urchin embryos
Journal:
Development
DOI:
10.1242/dev.205025
Associate Professor YAGUCHI, Shunsuke
Institute of Life and Environmental Sciences, University of Tsukuba
Specially Appointed Lecturer TSUYUZAKI, Koki
Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University
Professor YAMAMOTO, Takashi
Genome Editing Innovation Center, Hiroshima University
Associate Professor IKEO, Kazuho
DNA Data Analysis Laboratory, National Institute of Genetics
Institute of Life and Environmental Sciences
Development
Single-cell transcriptomic resources for tracing neurogenesis and cell fate specification in sea urchin embryos
26-Feb-2026