Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):E717-E726. doi: 10.1073/pnas.1620755114. Epub 2017 Jan 17.


Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules, few of which have been identified. Here, we quantified the global abundance of transcripts, proteins, and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach, we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions, including development, bioelectric signaling, and amino acid and lipid metabolism. Moreover, 32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus, the identification of proximodistal differences in levels of RNAs, proteins, and metabolites will facilitate future functional studies of positional memory during appendage regeneration.

Keywords: caudal fin; growth control; positional memory; regeneration; zebrafish.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animal Fins / physiology*
  • Animals
  • Female
  • Male
  • Metabolomics
  • Proteomics
  • Regeneration / physiology
  • Transcriptome
  • Zebrafish* / genetics
  • Zebrafish* / metabolism
  • Zebrafish* / physiology