Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
???displayArticle.abstract???
Identifying cell states during development from their mRNA profiles provides insight into their gene regulatory network. Here, we leverage the sea urchin embryo for its well-established gene regulatory network to interrogate the embryo using single cell RNA sequencing. We tested eight developmental stages in Strongylocentrotus purpuratus, from the eight-cell stage to late in gastrulation. We used these datasets to parse out 22 major cell states of the embryo, focusing on key transition stages for cell type specification of each germ layer. Subclustering of these major embryonic domains revealed over 50 cell states with distinct transcript profiles. Furthermore, we identified the transcript profile of two cell states expressing germ cell factors, one we conclude represents the primordial germ cells and the other state is transiently present during gastrulation. We hypothesize that these cells of the Veg2 tier of the early embryo represent a lineage that converts to the germ line when the primordial germ cells are deleted. This broad resource will hopefully enable the community to identify other cell states and genes of interest to expose the underpinning of developmental mechanisms.
Andrikou,
Myogenesis in the sea urchin embryo: the molecular fingerprint of the myoblast precursors.
2013, Pubmed,
Echinobase
Andrikou,
Myogenesis in the sea urchin embryo: the molecular fingerprint of the myoblast precursors.
2013,
Pubmed
,
Echinobase
Anishchenko,
SoxB2 in sea urchin development: implications in neurogenesis, ciliogenesis and skeletal patterning.
2018,
Pubmed
,
Echinobase
Annunziata,
Pattern and process during sea urchin gut morphogenesis: the regulatory landscape.
2014,
Pubmed
,
Echinobase
Bialkowska,
Krüppel-like factors in mammalian stem cells and development.
2017,
Pubmed
Briggs,
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.
2018,
Pubmed
Bruskin,
Accumulation in embryogenesis of five mRNAs enriched in the ectoderm of the sea urchin pluteus.
1981,
Pubmed
,
Echinobase
Butler,
Integrating single-cell transcriptomic data across different conditions, technologies, and species.
2018,
Pubmed
Cameron,
Macromere cell fates during sea urchin development.
1991,
Pubmed
,
Echinobase
Chen,
Effete-mediated degradation of Cyclin A is essential for the maintenance of germline stem cells in Drosophila.
2009,
Pubmed
Cho,
Cap-dependent translational inhibition establishes two opposing morphogen gradients in Drosophila embryos.
2006,
Pubmed
Clegg,
Maelstrom is required to position the MTOC in stage 2-6 Drosophila oocytes.
2001,
Pubmed
Davidson,
Specification of cell fate in the sea urchin embryo: summary and some proposed mechanisms.
1998,
Pubmed
,
Echinobase
Drabikowski,
ten-1, an essential gene for germ cell development, epidermal morphogenesis, gonad migration, and neuronal pathfinding in Caenorhabditis elegans.
2005,
Pubmed
Ettensohn,
Alx1, a member of the Cart1/Alx3/Alx4 subfamily of Paired-class homeodomain proteins, is an essential component of the gene network controlling skeletogenic fate specification in the sea urchin embryo.
2003,
Pubmed
,
Echinobase
Findley,
Maelstrom, a Drosophila spindle-class gene, encodes a protein that colocalizes with Vasa and RDE1/AGO1 homolog, Aubergine, in nuage.
2003,
Pubmed
Fink,
Three cell recognition changes accompany the ingression of sea urchin primary mesenchyme cells.
1985,
Pubmed
,
Echinobase
Foster,
Single cell RNA-seq in the sea urchin embryo show marked cell-type specificity in the Delta/Notch pathway.
2019,
Pubmed
,
Echinobase
Fujii,
Role of the nanos homolog during sea urchin development.
2009,
Pubmed
,
Echinobase
Garner,
Neurogenesis in sea urchin embryos and the diversity of deuterostome neurogenic mechanisms.
2016,
Pubmed
,
Echinobase
George,
Characterization and expression of a gene encoding a 30.6-kDa Strongylocentrotus purpuratus spicule matrix protein.
1991,
Pubmed
,
Echinobase
Gulati,
Single-cell transcriptional diversity is a hallmark of developmental potential.
2020,
Pubmed
Gustafson,
Exogenous RNA is selectively retained in the small micromeres during sea urchin embryogenesis.
2010,
Pubmed
,
Echinobase
Gustafson,
Post-translational regulation by gustavus contributes to selective Vasa protein accumulation in multipotent cells during embryogenesis.
2011,
Pubmed
,
Echinobase
Irish,
The Drosophila posterior-group gene nanos functions by repressing hunchback activity.
1989,
Pubmed
Juliano,
Nanos functions to maintain the fate of the small micromere lineage in the sea urchin embryo.
2010,
Pubmed
,
Echinobase
Klein,
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
2015,
Pubmed
Kraemer,
NANOS-3 and FBF proteins physically interact to control the sperm-oocyte switch in Caenorhabditis elegans.
1999,
Pubmed
Lai,
Repressive translational control in germ cells.
2013,
Pubmed
Lai,
Nanos1 functions as a translational repressor in the Xenopus germline.
2011,
Pubmed
Luo,
Xenopus germline nanos1 is translationally repressed by a novel structure-based mechanism.
2011,
Pubmed
Macosko,
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
2015,
Pubmed
Materna,
Notch and Nodal control forkhead factor expression in the specification of multipotent progenitors in sea urchin.
2013,
Pubmed
,
Echinobase
McClay,
Separation of ectoderm and endoderm from sea urchin pluteus larvae and demonstration of germ layer-specific antigens.
1979,
Pubmed
,
Echinobase
McClay,
Specificity of cell-cell interactions in sea urchin embryos. Appearance of new cell-surface determinants at gastrulation.
1977,
Pubmed
,
Echinobase
NULL,
What Is Your Conceptual Definition of "Cell Type" in the Context of a Mature Organism?
2017,
Pubmed
Oliveri,
Repression of mesodermal fate by foxa, a key endoderm regulator of the sea urchin embryo.
2006,
Pubmed
,
Echinobase
Oulhen,
Distinct transcriptional regulation of Nanos2 in the germ line and soma by the Wnt and delta/notch pathways.
2019,
Pubmed
,
Echinobase
Oulhen,
Retention of exogenous mRNAs selectively in the germ cells of the sea urchin requires only a 5'-cap and a 3'-UTR.
2013,
Pubmed
,
Echinobase
Oulhen,
Transient translational quiescence in primordial germ cells.
2017,
Pubmed
,
Echinobase
Oulhen,
Identifying gene expression from single cells to single genes.
2019,
Pubmed
,
Echinobase
Patmanidi,
Concise Review: Geminin-A Tale of Two Tails: DNA Replication and Transcriptional/Epigenetic Regulation in Stem Cells.
2017,
Pubmed
Peter,
The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage.
2010,
Pubmed
,
Echinobase
Poustka,
A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks.
2007,
Pubmed
,
Echinobase
Ransick,
Whole mount in situ hybridization shows Endo 16 to be a marker for the vegetal plate territory in sea urchin embryos.
1993,
Pubmed
,
Echinobase
Roegiers,
Staufen: a common component of mRNA transport in oocytes and neurons?
2000,
Pubmed
Saunders,
Mouse staufen genes are expressed in germ cells during oogenesis and spermatogenesis.
2000,
Pubmed
Siebert,
Stem cell differentiation trajectories in Hydra resolved at single-cell resolution.
2019,
Pubmed
Song,
The forkhead transcription factor FoxY regulates Nanos.
2012,
Pubmed
,
Echinobase
Soper,
Mouse maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis.
2008,
Pubmed
St Johnston,
Staufen, a gene required to localize maternal RNAs in the Drosophila egg.
1991,
Pubmed
Stuart,
Comprehensive Integration of Single-Cell Data.
2019,
Pubmed
Swartz,
Deadenylase depletion protects inherited mRNAs in primordial germ cells.
2014,
Pubmed
,
Echinobase
Takacs,
Expression of an NK2 homeodomain gene in the apical ectoderm defines a new territory in the early sea urchin embryo.
2004,
Pubmed
,
Echinobase
Tu,
Sea urchin Forkhead gene family: phylogeny and embryonic expression.
2006,
Pubmed
,
Echinobase
Tu,
Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus.
2014,
Pubmed
,
Echinobase
Urry,
Expression of spicule matrix proteins in the sea urchin embryo during normal and experimentally altered spiculogenesis.
2000,
Pubmed
,
Echinobase
Voronina,
Vasa protein expression is restricted to the small micromeres of the sea urchin, but is inducible in other lineages early in development.
2008,
Pubmed
,
Echinobase
Wang,
nanos function is essential for development and regeneration of planarian germ cells.
2007,
Pubmed
Wei,
The sea urchin animal pole domain is a Six3-dependent neurogenic patterning center.
2009,
Pubmed
,
Echinobase
Wessel,
Somatic cell conversion to a germ cell lineage: A violation or a revelation?
2021,
Pubmed
,
Echinobase
Wohlschlegel,
Expression of geminin as a marker of cell proliferation in normal tissues and malignancies.
2002,
Pubmed
Wu,
Cancer. Germ cell genes and cancer.
2010,
Pubmed
Yaguchi,
A Wnt-FoxQ2-nodal pathway links primary and secondary axis specification in sea urchin embryos.
2008,
Pubmed
,
Echinobase
Yaguchi,
ankAT-1 is a novel gene mediating the apical tuft formation in the sea urchin embryo.
2010,
Pubmed
,
Echinobase
Zazueta-Novoa,
Protein degradation machinery is present broadly during early development in the sea urchin.
2014,
Pubmed
,
Echinobase
