A single-cell RNA-seq analysis of Brachyury-expressing cell clusters suggests a morphogenesis-associated signal center of oral ectoderm in sea urchin embryos

Dev Biol. 2022 Mar;483:128-142. doi: 10.1016/j.ydbio.2022.01.005. Epub 2022 Jan 14.


Brachyury is a T-box family transcription factor and plays pivotal roles in morphogenesis. In sea urchin embryos, Brachyury is expressed in the invaginating endoderm, and in the oral ectoderm of the invaginating mouth opening. The oral ectoderm is hypothesized to serve as a signaling center for oral (ventral)-aboral (dorsal) axis formation and to function as a ventral organizer. Our previous results of a single-cell RNA-seq (scRNA-seq) atlas of early Strongylocentrotus purpuratus embryos categorized the constituent cells into 22 clusters, in which the endoderm consists of three clusters and the oral ectoderm four clusters (Foster et al., 2020). Here we examined which clusters of cells expressed Brachyury in relation to the morphogenesis and the identity of the ventral organizer. Our results showed that cells of all three endoderm clusters expressed Brachyury in blastulae. Based on expression profiles of genes involved in the gene regulatory networks (GRNs) of sea urchin embryos, the three clusters are distinguishable, two likely derived from the Veg2 tier and one from the Veg1 tier. On the other hand, of the four oral-ectoderm clusters, cells of two clusters expressed Brachyury at the gastrula stage and genes that are responsible for the ventral organizer at the late blastula stage, but the other two clusters did not. At a single-cell level, most cells of the two oral-ectoderm clusters expressed organizer-related genes, nearly a half of which coincidently expressed Brachyury. This suggests that the ventral organizer contains Brachyury-positive cells which invaginate to form the stomodeum. This scRNA-seq study therefore highlights significant roles of Brachyury-expressing cells in body-plan formation of early sea urchin embryos, though cellular and molecular mechanisms for how Brachyury functions in these processes remain to be elucidated in future studies.

Keywords: Archenteron invagination; Brachyury-expressing cell clusters; Endoderm; Oral ectoderm; Sea urchin embryos; Stomodeum invagination; The ventral organizer.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Blastula / metabolism
  • Ectoderm / cytology*
  • Ectoderm / embryology
  • Ectoderm / metabolism*
  • Embryonic Development / genetics*
  • Endoderm / embryology
  • Endoderm / metabolism
  • Fetal Proteins / metabolism*
  • Gastrula / metabolism
  • Gene Expression Regulation, Developmental*
  • Gene Regulatory Networks
  • RNA-Seq / methods*
  • Sea Urchins / embryology*
  • Sea Urchins / genetics*
  • Signal Transduction / genetics
  • Single-Cell Analysis / methods*
  • T-Box Domain Proteins / metabolism*


  • Fetal Proteins
  • T-Box Domain Proteins
  • Brachyury protein