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Published September 2017 | public
Journal Article

Regulatory states in the developmental control of gene expression


A growing body of evidence shows that gene expression in multicellular organisms is controlled by the combinatorial function of multiple transcription factors. This indicates that not the individual transcription factors or signaling molecules, but the combination of expressed regulatory molecules, the regulatory state, should be viewed as the functional unit in gene regulation. Here, I discuss the concept of the regulatory state and its proposed role in the genome-wide control of gene expression. Recent analyses of regulatory gene expression in sea urchin embryos have been instrumental for solving the genomic control of cell fate specification in this system. Some of the approaches that were used to determine the expression of regulatory states during sea urchin embryogenesis are reviewed. Significant developmental changes in regulatory state expression leading to the distinct specification of cell fates are regulated by gene regulatory network circuits. How these regulatory state transitions are encoded in the genome is illuminated using the sea urchin endoderm–mesoderms cell fate decision circuit as an example. These observations highlight the importance of considering developmental gene regulation, and the function of individual transcription factors, in the context of regulatory states.

Additional Information

© 2017 The Author. Published by Oxford University Press. Published: 24 April 2017. I wish to thank Deanna Thomas for her work in preparing the figures and Jonathan Valencia for providing the image showing gcm expression in the late embryo. I am deeply grateful to Eric Davidson for countless discussions over the years that contributed to the thoughts expressed here. This work was supported by National Institutes of Health Grant HD-037105.

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October 26, 2023