title: Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish.
abstract: 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.
authors.affiliation: Department of Pharmacology, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, WA 98109; jsr2137@uw.edu rtmoon@uw.edu.
authors.forename: Jeremy S
authors.identifier: 0000-0002-6981-6863
authors.initials: JS
authors.lastname: Rabinowitz
authors.affiliation: Department of Pharmacology, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, WA 98109.
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Robitaille
authors.affiliation: Department of Computer Science & Engineering, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109.
authors.forename: Yuliang
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Pharmacology, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, WA 98109.
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Ray
authors.affiliation: Departments of Anatomy/Cell Biology and Ophthalmology, Wayne State University School of Medicine, Detroit, MI 48201.
authors.forename: Ryan
authors.initials: R
authors.lastname: Thummel
authors.affiliation: Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109.
authors.forename: Haiwei
authors.initials: H
authors.lastname: Gu
authors.affiliation: Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109.
authors.forename: Danijel
authors.initials: D
authors.lastname: Djukovic
authors.affiliation: Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109.
authors.forename: Daniel
authors.initials: D
authors.lastname: Raftery
authors.affiliation: Department of Pharmacology, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, WA 98109.
authors.forename: Jason D
authors.initials: JD
authors.lastname: Berndt
authors.affiliation: Department of Pharmacology, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, WA 98109; jsr2137@uw.edu rtmoon@uw.edu.
authors.forename: Randall T
authors.initials: RT
authors.lastname: Moon
mesh_terms: D058500:Animal Fins / Q000502:physiology*; D000818:Animals; D005260:Female; D008297:Male; D055432:Metabolomics; D040901:Proteomics; D012038:Regeneration / Q000502:physiology; D059467:Transcriptome; D015027:Zebrafish / Q000235:genetics / Q000378:metabolism / Q000502:physiology
keywords: caudal fin; growth control; positional memory; regeneration; zebrafish