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Volume 6, Pages 38-54
Research Article

Transcriptional Profiling of Caudal Fin Regeneration in Zebrafish

Howard Hughes Medical Institute, Department of Cardiology and Department of Pediatrics, Children's Hospital, Department of Cell Biology, Harvard Medical School, 320 Longwood Avenue, Boston, MA 02115, USA

Received 5 March 2006; Revised 4 May 2006; Accepted 12 May 2006

Academic Editor: Marie-Andree Akimenko

Copyright © 2006 Michael Schebesta et al.


Regeneration of severed limbs in adult animals is restricted to urodele amphibians. Mammals, including humans, have very limited regenerative capabilities and even with proper treatment, only the tips of our digits can grow back. Teleost fish can regenerate amputated fins, the evolutionary ancestors of limbs. To elucidate the principles of limb-fin regeneration, we performed an Affymetrix microarray screen on regenerating caudal fins 12, 24, 48, and 72 h post amputation. Approximately 15,000 zebrafish transcripts were analyzed, identifying 829 transcripts as differentially expressed during regeneration. Of those, 563 were up-regulated and 266 were down-regulated. We constructed a comprehensive database containing expression data, functional assignment, and background information from the literature for each differentially expressed transcript. In order to validate our findings, we employed three approaches: (1) microarray expression analysis of genes previously implicated in fin regeneration, (2) RT-PCR analysis of genes newly identified as differentially expressed during regeneration, and (3) in situ hybridization of the up-regulated genes bambi, dlx5A, and her6. Moreover, we show that Smad 1/5/8 proteins, effector molecules of Bmp signaling, are phosphorylated during fin regeneration. Taken together, we provide a comprehensive database of fin regeneration that will serve as an important tool for understanding the molecular mechanisms of regeneration.