David R. McClay

Arthur S. Pearse Distinguished Professor of Biology

4102 French Science Center, Science Dr., Durham, NC 27708
Campus Box: 
Box 90338, Department of Biology, Durham, NC 27708-1000
(919) 613-8188
We ask how the embryo works. Prior to morphogenesis the embryo specifies each cell through transcriptional regulation and signaling. Our research builds gene regulatory networks to understand how that early specification works. We then ask how this specification programs cells for their morphogenetic movements at gastrulation, and how the cells deploy patterning information. Current projects examine 1) novel signal transduction mechanisms that establish and maintain embryonic boundaries mold the embryo at gastrulation; 2) specification of primary mesenchyme cells in such a way that they are prepared to execute an epithelial-mesenchymal transition, and then study mechanistically the regulation of that transition; 3) the specification of endoderm necessary for invagination of the archenteron; 4) formation of the oral/aboral ectoderm and the means by which patterning information is distributed three dimensionally around the embryo. That information is necessary for patterning and inducing skeletogenesis. Other projects examine neural tube folding with the goal of identifying genes associated with neural tube defects. Finally, a large current effort in systems biology is being expended with the goal of enlarging our knowledge of early networks and how they interact.


  • Ph.D., University of North Carolina - Chapel Hill 1971

  • M.S., University of Vermont 1965

  • B.S., Pennsylvania State University 1963

McClay, David R., Jacob Warner, Megan Martik, Esther Miranda, and Leslie Slota. “Gastrulation in the sea urchin.,” 136:195–218, 2020. https://doi.org/10.1016/bs.ctdb.2019.08.004. Full Text

Massri, Abdull J., Geoffrey R. Schiebinger, Alejandro Berrio, Lingyu Wang, Gregory A. Wray, and David R. McClay. “Methodologies for Following EMT In Vivo at Single Cell Resolution.Methods in Molecular Biology (Clifton, N.J.) 2179 (January 2021): 303–14. https://doi.org/10.1007/978-1-0716-0779-4_23. Full Text

McClay, David R. “Perspective on Epithelial-Mesenchymal Transitions in Embryos.Methods in Molecular Biology (Clifton, N.J.) 2179 (January 2021): 7–12. https://doi.org/10.1007/978-1-0716-0779-4_2. Full Text

Massri, Abdull, Laura Greenstreet, Anton Afanassiev, Alejandro Berrio Escobar, Gregory Wray, Geoffrey Schiebinger, and David McClay. “Developmental Single-cell transcriptomics in the Lytechinus variegatus Sea Urchin Embryo,” November 13, 2020. https://doi.org/10.1101/2020.11.12.380675. Full Text Open Access Copy

Davidson, Phillip L., Haobing Guo, Lingyu Wang, Alejandro Berrio, He Zhang, Yue Chang, Andrew L. Soborowski, David R. McClay, Guangyi Fan, and Gregory A. Wray. “Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses.Genome Biology and Evolution 12, no. 7 (July 2020): 1080–86. https://doi.org/10.1093/gbe/evaa101. Full Text

Yang, Jing, Parker Antin, Geert Berx, Cédric Blanpain, Thomas Brabletz, Marianne Bronner, Kyra Campbell, et al. “Guidelines and definitions for research on epithelial-mesenchymal transition.Nature Reviews. Molecular Cell Biology 21, no. 6 (June 2020): 341–52. https://doi.org/10.1038/s41580-020-0237-9. Full Text

Slota, Leslie A., Esther Miranda, Brianna Peskin, and David R. McClay. “Developmental origin of peripheral ciliary band neurons in the sea urchin embryo.Developmental Biology 459, no. 2 (March 2020): 72–78. https://doi.org/10.1016/j.ydbio.2019.12.011. Full Text

George, Andrew N., and David R. McClay. “Methods for transplantation of sea urchin blastomeres.Methods in Cell Biology 150 (January 2019): 223–33. https://doi.org/10.1016/bs.mcb.2018.11.012. Full Text

McClay, David R., Esther Miranda, and Stacy L. Feinberg. “Neurogenesis in the sea urchin embryo is initiated uniquely in three domains.Development (Cambridge, England) 145, no. 21 (November 9, 2018). https://doi.org/10.1242/dev.167742. Full Text


Lyons, Diedre, Dan McIntyre, and David R. McClay. “Ectodermal inputs into patterning skeletogenesis.” In Integrative and Comparative Biology, 54:E128–E128. OXFORD UNIV PRESS INC, 2014.

Lyons, Deirdre C., and David R. Mcclay. “Programmed cell fusion of PMCs during skeletal development in the sea urchin Lytechinus variegatus.” In Integrative and Comparative Biology, 52:E287–E287. OXFORD UNIV PRESS INC, 2012.

McIntyre, Daniel C., Winn Seay, and David R. McClay. “IrxA expression and function in establishing the sea urchin endoderm–ectoderm boundary.” In Developmental Biology, 344:469–469. Elsevier BV, 2010. https://doi.org/10.1016/j.ydbio.2010.05.226. Full Text

McClay, David R., Jenifer C. Croce, Shu-Yu Wu, Wendy S. Beane, and Katherine D. Walton. “Gene regulatory networks governing morphogenesis.” In Developmental Biology, 319:477–477. Elsevier BV, 2008. https://doi.org/10.1016/j.ydbio.2008.05.043. Full Text

Croce, Jenifer C., and David R. McClay. “A new role for an old gene: Brachyury and the subdivision of the endomesoderm.” In Developmental Biology, 306:294–294. Elsevier BV, 2007. https://doi.org/10.1016/j.ydbio.2007.03.065. Full Text

Beane, Wendy S., and David R. McClay. “Patterning the sea urchin skeleton: A role for calcium signaling.” In Developmental Biology, 306:400–400. Elsevier BV, 2007. https://doi.org/10.1016/j.ydbio.2007.03.599. Full Text

Wu, Shu-Yu, and David R. McClay. “Constructing the EMT regulatory network of PMCs in sea urchin embryos.” In Developmental Biology, 306:435–435. Elsevier BV, 2007. https://doi.org/10.1016/j.ydbio.2007.03.673. Full Text

Beane, Wendy S., and David R. McClay. “Clearing the way: The small GTPase RhoA and endomesodermal specification.” In Developmental Biology, 295:411–12. Elsevier BV, 2006. https://doi.org/10.1016/j.ydbio.2006.04.264. Full Text

Bradham, Cynthia A., Albert J. Poustka, and David R. McClay. “Chordin is required for neural but not axial specification in sea urchin embryos.” In Developmental Biology, 295:331–331. Elsevier BV, 2006. https://doi.org/10.1016/j.ydbio.2006.04.035. Full Text

Selected Grants

Genetic and Genomics Training Grant awarded by National Institutes of Health (Mentor). 2020 to 2025

Embryonic Cell Recognition: Specificity Determinants awarded by National Institutes of Health (Principal Investigator). 1980 to 2023

Training Program in Developmental and Stem Cell Biology awarded by National Institutes of Health (Mentor). 2001 to 2022

Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health (Mentor). 2005 to 2021

How Gene Regulatory Networks Connect to Development awarded by California Institute of Technology (Principal Investigator). 2009 to 2021

Genetics Training Grant awarded by National Institutes of Health (Mentor). 1979 to 2020

Organization and Function of Cellular Structure awarded by National Institutes of Health (Mentor). 1975 to 2020

Lightsheet Imaging System awarded by National Institutes of Health (Major User). 2016 to 2017

Illumina Hi-Seq 2000 Sequencing System awarded by National Institutes of Health (Major User). 2012 to 2013

Mechanism of a novel cause of spina bifida awarded by National Institutes of Health (Consultant). 2009 to 2012