Open Access Highly Accessed Research article

Gene expression throughout a vertebrate's embryogenesis

Goran Bozinovic15, Tim L Sit2, David E Hinton3 and Marjorie F Oleksiak4*

Author Affiliations

1 Department of Environmental and Molecular Toxicology, Box 7633, North Carolina State University, Raleigh, NC 27695-7633, USA

2 Department of Plant Pathology, Box 7342, North Carolina State University, Raleigh, NC 27695-7342, USA

3 Nicholas School of the Environment, Duke University, A333 LSRC, Box 90328, Durham, NC 27708, USA

4 Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA

5 Current Address: Division of Biological Sciences, York Hall 4070B, 9500 Gilman Drive, University of California at San Diego, La Jolla, CA 92093, USA

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BMC Genomics 2011, 12:132  doi:10.1186/1471-2164-12-132

Published: 28 February 2011



Describing the patterns of gene expression during embryonic development has broadened our understanding of the processes and patterns that define morphogenesis. Yet gene expression patterns have not been described throughout vertebrate embryogenesis. This study presents statistical analyses of gene expression during all 40 developmental stages in the teleost Fundulus heteroclitus using four biological replicates per stage.


Patterns of gene expression for 7,000 genes appear to be important as they recapitulate developmental timing. Among the 45% of genes with significant expression differences between pairs of temporally adjacent stages, significant differences in gene expression vary from as few as five to more than 660. Five adjacent stages have disproportionately more significant changes in gene expression (> 200 genes) relative to other stages: four to eight and eight to sixteen cell stages, onset of circulation, pre and post-hatch, and during complete yolk absorption. The fewest differences among adjacent stages occur during gastrulation. Yet, at stage 16, (pre-mid-gastrulation) the largest number of genes has peak expression. This stage has an over representation of genes in oxidative respiration and protein expression (ribosomes, translational genes and proteases). Unexpectedly, among all ribosomal genes, both strong positive and negative correlations occur. Similar correlated patterns of expression occur among all significant genes.


These data provide statistical support for the temporal dynamics of developmental gene expression during all stages of vertebrate development.