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Published November 15, 2015 | public
Journal Article Open

Genome-wide assessment of differential effector gene use in embryogenesis


Six different populations of cells were isolated by FACS from disaggregated late blastula and gastrula stage sea urchin embryos according to the regulatory states expressed in these cells, as reported by recombineered BACs producing fluorochromes. Transcriptomes recovered from these embryonic cell populations revealed striking, early differential expression of large cohorts of effector genes. The six cell populations were presumptive pigment cells, presumptive neurogenic cells, presumptive skeletogenic cells, cells from the stomodeal region of the oral ectoderm, ciliated band cells, and cells from the endoderm/ectoderm boundary that will give rise both to hindgut and to border ectoderm. Transcriptome analysis revealed that each of these domains specifically expressed several hundred effector genes at significant levels. Annotation indicates the qualitative individuality of the functional nature of each cell population, even though they were isolated from embryos only 1 to 2 days old. In no case was more than a tiny fraction of the transcripts enriched in one population also enriched in any other of the six populations studied. As was particularly clear in the cases of the presumptive pigment, neurogenic, and skeletogenic cells, all three of which represent precociously differentiating cell types of this embryo, most specifically expressed genes of given cell types are not significantly expressed at all in the other cell types. Thus at the effector gene level a dramatic, cell type specific pattern of differential gene regulation is established well before any significant embryonic morphogenesis has occurred.

Additional Information

© 2015 Company of Biologists. Received June 22, 2015. Accepted September 16, 2015. Posted online before print September 28, 2015. This work is dedicated to the memory of our mentor Eric H. Davidson, 1937–2015. Many collaborators contributed their invaluable expertise to this project. We would particularly like to acknowledge the expert assistance of Shelley Diamond and her assistants Diana Perez and Pat Koen in developing an efficacious FACS protocol for sea urchin embryo cells; the generous provision by Dr. Enhu Li of the in situ hybridization images in Fig.1 of this paper; Dr. Andrew Ransick for kindly providing the gcm cis-reg construct used to isolate pigment cells and related micrographs used in Fig.1A1 & 2A1; and the multiple contributions of Erika Vielmas, who by microscopic examination authenticated the expression patterns of the injected BACs used to isolate the various cell populations, and assisted in miscellaneous aspects of this study. This work was supported by a grant from the NICHD (National Institute of Child Health and Development), HD067454; and from NIGMS (National Institute of General Medical Sciences), RR015044. Author Contributions: J.C.B. and E.H.D. designed the research; J.C.B. and C.C. performed the research; J.C.B., Q.T. and E.H.D. analyzed the data; and J.C.B. and E.H.D. wrote the paper.

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August 20, 2023
August 20, 2023