Research interests

Physiogenomic Control of Sea Urchin Embryogenesis

The Coffman lab uses the sea urchin embryo as a model system to examine physiogenomic systems that control cell fate during animal development. We are particularly interested in gene regulatory networks that coordinate cell proliferation, survival, and differentiation. These networks are often susceptible to environmental perturbations, and compromised by genetic mutations that give rise to cancer and other diseases.

Much of our effort is currently focused on the Runx family of transcriptional regulatory proteins. This family plays an essential role in development and contributes to leukemia and other forms of cancer. Since many gene regulatory interactions are evolutionarily conserved, what we learn about Runx function and regulation in sea urchins will shed light on how Runx genes both control development and contribute to cancer in humans.

A second project concerns axis specification - the symmetry breaking process whereby the initial spatial coordinates of the body plan are established. In this context we are studying the role of mitochondrial distribution and redox state in modulating the activities of regulatory proteins involved in specifying the secondary (oral-aboral) axis of the sea urchin embryo.

Publications

• Knowlton, P., and Coffman, J.A. (2007). A Runx protein is required for cell proliferation in late blastula stage embryos of the sea urchin, Strongylocentrotus purpuratus. MDIBL Bulletin 46: 65-67.
• Nam, J., Su, Y.-H., Lee, P.Y., Robertson A. J., Coffman, J. A., and Davidson, E.H. (2007). Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network. Dev. Biol. 306: 860-869.
• Robertson, A.J., Dickey-Sims, C., Ransick, A., Rupp, D.E., McCarthy, J.J., and Coffman, J.A. (2006). CBFβ is a facultative Runx partner in the sea urchin embryo. BMC Biol. 4: 4. (“Editor’s Choice” in the BioMed Central Update)
• The Sea Urchin Genome Sequencing Consortium (2006). The genome of the sea urchin Strongylocentrotus purpuratus. Science. 314: 941-952.
• Bradham, C.A., Beane, W.S., Arnone, M.I., Rizzo, F., Coffman, J.A., Mushegian, A., Goel, M., Morales, J., Geneviere, A-M., Lapraz, F., Robertson, A.J., Kelkar, H., Loza-Coll, M., Townley, I.R., Raisch, M., Roux, M.M., Lepage, T., Gache, C., McClay, D.R., and Foltz, K.R. (2006). The sea urchin kinome: a first look. Dev. Biol. 300: 180-193.
• Byrum, C.A., Walton, K., Robertson, A.J., Carbonneau, S., Thomason, R., Bradham, C.A., Coffman, J.A., and McClay, D.R. (2006). Protein tyrosine and ser-thr phosphatases in the sea urchin, Strongylocentrotus purpuratus: identification and potential functions. Dev. Biol. 300: 194-218.
• Fernandez-Guerra, A., Aze, A., Morales, J., Mulner-Lorillon, O., Cosson, B., Cormier, P., Bradham, C., Adams, N., Robertson, A.J., Marzluff, W.F., Coffman, J.A., and Genevière, A.M. (2006). The genomic repertoire for cell cycle control and DNA metabolism in S. purpuratus. Dev. Biol. 300: 238-251.
• Robertson, A.J., Croce, J., Carbonneau, S., Voronina, E., Miranda, E., McClay, D.R. and Coffman, J.A. (2006). The genomic underpinnings of apoptosis in Strongylocentrotus purpuratus. Dev. Biol. 300: 321-334.
• Stewart, P.L., Makabi, M., Lang, J., Dickey-Sims, C., Robertson, A.J., Coffman, J.A., and Suprenant, K.A. (2005). Sea urchin vault structure, composition, and differential localization during development. BMC Dev. Biol. 5: 3. (“Image of the Month” selection)
• Dickey-Sims, C., Robertson, A.J., Rupp, D.E., McCarthy, J.J., and Coffman, J.A. (2005). Runx-dependent expression of PKC is critical for cell survival in the sea urchin embryo. BMC Biol. 3: 18. (“Editor’s Choice” in the BioMed Central Update; flagged as “Highly Accessed” in the BioMed Central table of contents)
• Robertson, A.J., Howard, J.T., Dominski, Z., Schnackenberg, B.J., Sumerel, J.L., McCarthy, J.J., Coffman, J.A., and Marzluff, W.F. (2004). The sea urchin stemloop binding protein: a maternally expressed protein that likely functions in expression of multiple classes of histone mRNA. Nucleic Acids Res. 32: 811-818.
• Coffman, J.A., Dickey-Sims, C., Haug, J.S., McCarthy, J.J., and Robertson, A.J. (2004). Evaluation of developmental phenotypes produced by morpholino antisense targeting of a sea urchin Runx gene. BMC Biol. 2: 6. (“Editor’s Choice” in the BioMed Central Update)
• Coffman, J.A., McCarthy, J.J., Dickey-Sims, C., and Robertson, A.J. (2004). Oral-aboral axis specification in the sea urchin embryo. II. Mitochondrial distribution and redox state contribute to establishing polarity in Strongylocentrotus purpuratus. Dev. Biol. 273: 160-171.
• Rennert, J., Coffman, J.A., Mushegian, A.R., and Robertson, A.J. (2003). The evolution of Runx genes. I. A comparative study of sequences from phylogenetically diverse model organisms. BMC Evol. Biol. 3: 4.
• Robertson, AJ., Dickey, C.E., McCarthy, J.J., and Coffman, J.A. (2002). The expression of SpRunt during sea urchin embryogenesis. Mech. Dev. 117: 327-330.
• Coffman, J.A., and Davidson, E.H. (2001). Oral-aboral axis specification in the sea urchin embryo. I. Axis entrainment by respiratory asymmetry. Dev. Biol. 230: 18-28. (Cover Photo)
• Calzone, F.J., Grainger, J., Coffman, J.A., and Davidson, E.H. (1997). Extensive maternal representation of DNA-binding proteins that interact with regulatory target sites of the Strongylocentrotus purpuratus CyIIIa gene. Mol. Mar. Biol. Biotechnol. 6: 79-83.
• Harrington, M.G., Coffman, J.A., and Davidson, E.H. (1997). Covalent variation is a general property of transcription factors in the sea urchin embryo. Mol. Mar. Biol. Biotechnol. 6: 153-162.
• Coffman, J.A., Kirchhamer, C.V., Harrington, M.G., and Davidson, E.H. (1997). SpMyb functions as an intramodular repressor to regulate spatial expression of CyIIIa in sea urchin embryos. Development 124: 4717-4727.
• Coffman, J.A., Kirchhamer, C.V., Harrington, M.G., and Davidson, E.H. (1996). SpRunt-1, a new member of the runt-domain family of transcription factors, is a positive regulator of the aboral ectoderm-specific CyIIIa gene in sea urchin embryos. Dev. Biol. 174: 43-54.
• Zeller, R.W., Coffman, J.A., Harrington, M.G., Britten, R.J., and Davidson, E.H. (1995). SpGCF1, a sea urchin embryo DNA binding protein, exists as five nested variants encoded by a single mRNA. Dev. Biol. 169: 713-727.
• Char, B.R., Bell, J.R., Dovola, J., Coffman, J.A., Harrington, M., Beccerra, J.C., Davidson, E.H., Calzone, F.J., and Maxson, R. (1993). SpOct, a gene encoding the major octamer-binding protein in sea urchin embryos: Expression profile, evolutionary relationships, and DNA binding of expressed protein. Dev. Biol. 158: 350-363.
• Coffman, J.A., Moore, J.G., Calzone, F.J., Britten, R.J., Hood, L.E., and Davidson, E.H. (1992). Automated sequential affinity chromatography of sea urchin embryo DNA binding proteins. Mol. Mar. Biol. Biotechnol. 1: 136-146.
• Harrington, M.G., Coffman, J.A., Calzone, F.J., Hood, L.E., Britten, R.J., and Davidson, E.H. (1992). Complexity of sea urchin embryo nuclear proteins that contain basic domains. Proc. Natl. Acad. Sci. USA 89: 6252-6256.
• Hardin, J., Coffman, J.A., Black, S.D., and McClay, D.R. (1992). Commitment along the dorsoventral axis of the sea urchin embryo is altered in response to NiCl2. Development 116: 671-685.

Community/University Service

Manuscript reviewer for Developmental Biology, Development, Mechanisms of Development,   Development Growth and Differentiation, International Journal of Developmental Biology, Molecular Biology and Evolution, Nucleic Acids Research, PNAS, Comparative Biochemistry and Physiology, International Journal of Cancer, BMC Molecular Biology, Acta Biotheoretica, BioEssays, Proceedings of the Royal Society: Biological Sciences, Biological Bulletin, FEBS Letters, Experimental Cell Research, and Genome Biology

Grant reviewer for the National Science Foundation (USA), Breast Cancer Campaign (UK), Association for International Cancer Research (UK), Bi-national Science Foundation (Israel-USA), Israel Science Foundation (Israel), and Biomedical Research Council (Singapore) 

• 2001 to 2001 — Community Service — Sea Urchin Genome Advisory Group
• 2002 to 2002 — Community Service — Co-organizer, Developmental Biology of the Sea Urchin XIV Conference
• 2005 to 2006 — Community Service — Coordinator, Sea Urchin Genome Annotation Consortium
• 2005 to 2005 — Community Service — NSF Developmental Systems (Animal and Evolution) Advisory Panel
• 2005 to 2005 — Community Service — NIH NCI P01 Cluster Review, Genomic Instability Special Emphasis Panel
• 2006 to 2007 — Community Service — NIH Neurogenesis and Cell Fate Study Section
• 2007 to 2007 — Community Service — NIH NICHD Initial Review Group, Developmental Biology Subcommittee

Grants

• 2005 to 2010 — — Control of cell proliferation by Runx proteins from NIH-R01 GM070840
• 2007 to 2010 — — Redox-sensitive developmental pathways and gene regulatory networks from NIH-R01 ES016722