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Development. 2015 Nov 15;142(22):3892-901. doi: 10.1242/dev.127746. Epub 2015 Sep 28.

Genome-wide assessment of differential effector gene use in embryogenesis.

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Division of Biology and Bioengineering, Caltech, 1200 East California Boulevard, Pasadena, CA 91125, USA
Division of Biology and Bioengineering, Caltech, 1200 East California Boulevard, Pasadena, CA 91125, USA.
Department of Biology, Valdosta State University, Valdosta, GA 31698, USA.


Six different populations of cells were isolated by fluorescence-activated cell sorting from disaggregated late blastula- and gastrula-stage sea urchin embryos according to the regulatory states expressed in these cells, as reported by recombineered bacterial artificial chromosomes 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 indicated the qualitative individuality of the functional nature of each cell population, even though they were isolated from embryos only 1-2 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.


Effector gene expression; Embryonic gene regulation; FACS embryonic cell populations; Sea urchin embryos

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