Ken Prehoda
Scott Stewart

BS, Biochemistry, University of Washington
PhD, Biological Chemistry, University of Michigan
Post-doctoral studies, Stanford University and the Salk Institute


Research Interests

The ability of humans to regenerate lost or an amputated body part is confined to the realms of science fiction and fantasy. Yet for centuries biologists have observed the astounding ability of certain animals, such as salamanders and teleost fish, which can do what is seemingly impossible: re-grow amputated body parts In fact, a near perfect copy of the amputated body part is formed by this process, called epimorphic regeneration, including the maintenance of anterior/posterior and dorsal/ventral identity, pigmentation, and size. This phenomenon of epimorphic regeneration is typically broken down into three steps. First, a wound epidermis is formed at the site of damage by migrating epithelial cells that seals the wound from the environment. Next, disorganization and dedifferentiation of tissue near the wound results in the creation of a mass of undifferentiated or differentiated cells, known as the blastema. Then, proliferation of blastema cells, concomitant with patterning and differentiation, results in the regeneration of the amputated portions of the damaged tissue.

The model organism we use to study tissue regeneration is the zebrafish, Danio rerio. The zebrafish exhibits an outstanding ability to regenerate different parts of its anatomy, including any of the paired and unpaired fins, the heart ventricle and the spinal cord. Zebrafish is particularly useful for studies on regeneration since it has short generation times, which make experiments requiring large number of animals feasible, and it has a fully sequenced and annotated genome. The zebrafish caudal fin is an established model of regeneration of a complex tissue that is easy to amputate, is not required for viability, and completely regenerates in a short time frame.

Stewart research

2 days after fin amputation, regenerating tissue becomes visible (left image). By 10 days after fin amputation, the fin has completely regenerated (right image).

A hallmark of epimorphic regeneration is the reactivation of silenced developmental regulatory genes that previously functioned during embryonic patterning. How can a gene be inactive for 1-2 years, in the case of a zebrafish caudal fin, and then be reactivated in just hours after amputatation? A gene silencing mechanism that may poise loci for reactivation has been described in ES cells in which nucleosomes near the transcription start sites of these silenced loci are decorated with trimethyl lysine 27 histone H3 (me3K27 H3) catalyzed by the Polycomb Repressive Complex 2, PRC2. In some cases both trimethyl lysine 4 histone H3 (me3K4 H3), a product of Trithorax activity, and me3K27 H3 are observed at transcription start sites of developmental regulatory genes, thus creating a “bivalent” histone code that appears to poise these loci for in embryonic stem (ES) cells. Similarly, our recent studies indicate that many developmental regulatory genes genes contain silent promoters decorated with a bivalent me3K4/me3K27 H3 domain. During regeneration of the zebrafish caudal fin, transcription activation of these promoters occurs in part by removal of repressive PcG-dependent me3K27 H3 which is likely mediated by histone demethylases, such as Kdm6b.1. Our observations support a model in which the zebrafish maintains a normal, non-regenerating gene expression program in the caudal fin which contributes to tissue homeostasis. Unlike non-regenerating animals, this gene expression program is switched after injury to the animal through the actions of plastic epigenetic mechanisms, including reversible histone modifications. Our results suggest that demethylation of me3K27 H3 contributes to gene expression in regenerating caudal fin. Current directions include examining how signals generated by fin amputation alter chromatin remodeling, gene activation, and cellular dedifferentiation.

Selected Publications

Stewart S, Sun ZY, Ispizua-Belmonte JC. A Histone Demethylase is Needed for Regeneration in Zebrafish. Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19889-94.

Stewart S, Rojas A, Ispizua-Belmonte JC. Bioelectricity and Epimorphic Regeneration. Bioessays. 2007 Nov; 29(11):1133-7

Stewart S, Fang G. Anaphase-Promoting Complex/Cyclosome Controls the Stability of TPX2 during Mitotic Exit. Mol Cell Biol. 2005 Dec;25(23):10516-27.

Stewart S, Fang G. Destruction box-dependent degradation of Aurora B is mediated by the Anaphase-Promoting Complex/Cyclosome and Cdh1. Cancer Res. 2005 Oct 1;65(19):8730-5.

Howell BJ, Moree B, Farrar EM, Stewart S, Fang G, Salmon ED. Spindle Checkpoint Protein Dynamics at Kinetochores in Living Cells. Current Biology. 2004 June 8 14(11) 953-964.

Department of Physics | Department of Chemistry | Department of Biology | UO Life Sciences | University of Oregon