title: Translational profiling of retinal ganglion cell optic nerve regeneration in Xenopus laevis.
abstract: Unlike adult mammals, adult frogs regrow their optic nerve following a crush injury, making Xenopus laevis a compelling model for studying the molecular mechanisms that underlie neuronal regeneration. Using Translational Ribosome Affinity Purification (TRAP), a method to isolate ribosome-associated mRNAs from a target cell population, we have generated a transcriptional profile by RNA-Seq for retinal ganglion cells (RGC) during the period of recovery following an optic nerve injury. Based on bioinformatic analysis using the Xenopus laevis 9.1 genome assembly, our results reveal a profound shift in the composition of ribosome-associated mRNAs during the early stages of RGC regeneration. As factors involved in cell signaling are rapidly down-regulated, those involved in protein biosynthesis are up-regulated alongside key initiators of axon development. Using the new genome assembly, we were also able to analyze gene expression profiles of homeologous gene pairs arising from a whole-genome duplication in the Xenopus lineage. Here we see evidence of divergence in regulatory control among a significant proportion of pairs. Our data should provide a valuable resource for identifying genes involved in the regeneration process to target for future functional studies, in both naturally regenerative and non-regenerative vertebrates.
authors.affiliation: Department of Biology, Washington and Lee University, Lexington, VA, United States.
authors.forename: G B
authors.initials: GB
authors.lastname: Whitworth
authors.affiliation: Department of Biology, Washington and Lee University, Lexington, VA, United States.
authors.forename: B C
authors.initials: BC
authors.lastname: Misaghi
authors.affiliation: Department of Biology, Washington and Lee University, Lexington, VA, United States.
authors.forename: D M
authors.initials: DM
authors.lastname: Rosenthal
authors.affiliation: Johns Hopkins University School of Medicine, Solomon H. Snyder Dept. of Neuroscience and Hugo Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States.
authors.forename: E A
authors.initials: EA
authors.lastname: Mills
authors.affiliation: Department of Biology, Washington and Lee University, Lexington, VA, United States.
authors.forename: D J
authors.initials: DJ
authors.lastname: Heinen
authors.affiliation: Department of Biology, Washington and Lee University, Lexington, VA, United States.
authors.forename: A H
authors.initials: AH
authors.lastname: Watson
authors.affiliation: Department of Biology, Washington and Lee University, Lexington, VA, United States.
authors.forename: C W
authors.initials: CW
authors.lastname: Ives
authors.affiliation: Department of Biology, Washington and Lee University, Lexington, VA, United States.
authors.forename: S H
authors.initials: SH
authors.lastname: Ali
authors.affiliation: Department of Biology, Washington and Lee University, Lexington, VA, United States.
authors.forename: K
authors.initials: K
authors.lastname: Bezold
authors.affiliation: Johns Hopkins University School of Medicine, Solomon H. Snyder Dept. of Neuroscience and Hugo Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States.
authors.forename: N
authors.initials: N
authors.lastname: Marsh-Armstrong
authors.affiliation: Department of Biology, Washington and Lee University, Lexington, VA, United States. Electronic address: watsonf@wlu.edu.
authors.forename: F L
authors.initials: FL
authors.lastname: Watson
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D030801:Animals, Genetically Modified; D005136:Eye Proteins / Q000096:biosynthesis* / Q000235:genetics; D005786:Gene Expression Regulation; D063990:Gene Ontology; D058977:Molecular Sequence Annotation; D009409:Nerve Crush; D009416:Nerve Regeneration / Q000502:physiology*; D009419:Nerve Tissue Proteins / Q000096:biosynthesis* / Q000235:genetics; D020221:Optic Nerve Injuries / Q000503:physiopathology*; D012333:RNA, Messenger / Q000235:genetics / Q000302:isolation & purification; D012165:Retinal Ganglion Cells / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D017386:Sequence Homology, Amino Acid; D015398:Signal Transduction; D029867:Xenopus Proteins / Q000096:biosynthesis* / Q000235:genetics; D014982:Xenopus laevis / Q000235:genetics* / Q000502:physiology
chemical_list: D005136:Eye Proteins; D009419:Nerve Tissue Proteins; D012333:RNA, Messenger; D029867:Xenopus Proteins
keywords: Expression profile; Optic nerve crush injury; TRAP