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

• 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.

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.