Translational profiling of retinal ganglion cell optic nerve regeneration in Xenopus laevis

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...

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Bibliographic Details
Published in:Developmental biology 2017-06, Vol.426 (2), p.360-373
Main Authors: Whitworth, G.B., Misaghi, B.C., Rosenthal, D.M., Mills, E.A., Heinen, D.J., Watson, A.H., Ives, C.W., Ali, S.H., Bezold, K., Marsh-Armstrong, N., Watson, F.L.
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Animals
Animals, Genetically Modified
Expression profile
Eye Proteins - biosynthesis
Eye Proteins - genetics
Gene Expression Regulation
Gene Ontology
Molecular Sequence Annotation
Nerve Crush
Nerve Regeneration - physiology
Nerve Tissue Proteins - biosynthesis
Nerve Tissue Proteins - genetics
Optic nerve crush injury
Optic Nerve Injuries - physiopathology
Retinal Ganglion Cells - metabolism
Ribosomes - metabolism
RNA, Messenger - genetics
RNA, Messenger - isolation & purification
Sequence Alignment
Sequence Analysis, RNA
Sequence Homology, Amino Acid
Signal Transduction
TRAP
Xenopus laevis - genetics
Xenopus laevis - physiology
Xenopus Proteins - biosynthesis
Xenopus Proteins - genetics
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Summary: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. •Generated TRAP expression profiles for retinal ganglion cells in an adult injury model.•RNA-Seq reveals down-regulation in cell signaling and cell-type specific factors after injury.•Injury leads to up-regulation in protein biosynthesis genes and initiators of axon development.•Sequence alignment to new gene models shows evidence for divergent regulation of homeolog pairs.•RNA-Seq data are available through public repository and interactive web application.
ISSN:0012-1606
1095-564X
DOI:10.1016/j.ydbio.2016.06.003